Fine mapping and candidate gene analysis of a novel PANICLE AND SPIKELET DEGENERATION gene in rice

To better understand the molecular mechanisms that regulate inflorescence and flower architecture, we characterized the rice panicle and spikelet degeneration (psd) mutant, which exhibited small panicles with a reduced number of primary and secondary branches. The psd mutant had few spikelets per panicle, and they were deformed and could not form seeds. The psd mutant had a unique panicle organization phenotype that was not present in other aberrant panicle organization mutants. Genetic analysis revealed that the mutation was controlled by a single recessive gene. A map-based cloning strategy was employed to isolate the PSD locus. The PSD locus was initially located between RM13046 and RM5356 on chromosome 2. Recessive individuals (n = 7307) in F2 mapping populations from two crosses between heterozygous Psdpsd plants and two indica rice varieties, IR28 and 93-11, were used to finely map the PSD locus. The PSD locus was mapped to a 14.6 kb region between two newly developed dCAPS markers, dC7 and dC8, within BAC OJ1115_D03. The candidate regions harbored two ORFs, Os02g0284500 and Os02g0284600. Sequence analysis revealed that only one single amino acid substitution mutation in the Os02g0284500 gene in the candidate region, which altered the predicted three-dimensional Os02g0284500 protein structure. A tetra-primer amplification refractory mutation system-PCR marker, TP-psd, was developed from the psd mutant mutation site. All 7307 homozygote recessive plants in the two F2 populations showed the same band pattern as that of psdpsd. This suggested that Os02g0284500 is most likely the PSD gene. Our results provide a basis for future functional PSD studies.