Identification and characterization of the stunted sterile (ss) mutant in rice

Background Proper organ development is pivotal for normal rice growth and production. Many genes are involved in this process, and these genes provide a basis for rice breeding. Objective To identify a novel mutation causing developmental defects in rice. Methods The phenotype of a rice mutant, stunted sterile ( ss ), identified from the japonica rice cultivar Samkwang treated with N -methyl- N -nitrosourea, was characterized, including anatomical and pollen activity analyses. A genetic analysis and fine mapping were performed to identify a candidate locus, followed by a sequence analysis to determine the causal mutation for the phenotype. Results Compared with wild-type plants, the mutant exhibited a 34% reduction in height, 46% reduction in flag leaf width, and complete panicle sterility. Cell proliferation in the leaf and pollen viability were significantly inhibited in the mutant. The mutant phenotypes were controlled by a single recessive gene that was fine-mapped to an 84 kb region between two SNP markers on the short arm of chromosome 5. A candidate gene analysis determined that the mutant carries an 11 bp insertion in the coding region of LOC_Os05g03550 , which encodes a protein containing two SANT domains, resulting in a premature termination codon before the conserved domain. Conclusions We identified a novel rice gene, Stunted sterile , involved in the regulation of various developmental processes. Our findings improve our understanding of the role of chromatin remodeling in organ development and have implications for breeding owing to the broad effects of the gene on plant growth.