Characterization and application of the qPL6.2 in regulating panicle length of rice (Oryza sativa L.)

Panicle length (PL) is one of the most important agronomic traits of rice; it determines panicle architecture and strongly affects grain yield and quality. Although several genes related to PL quantitative trait loci have been identified, PL has not been well characterized genetically, and its contribution to breeding and genetic improvement is unknown. Herein, we identified a novel quantitative trait locus for PL, i.e., qPL6.2, from single fragment substitution line P50, and mapped it to a region of 232.29-kb. The mapped region harbored 28 candidate genes, 7 of which were expressed more in young panicles than in other tissues. Further analysis of gene-knockout plants revealed LOC_Os06g06490 as a putative candidate gene of qPL6.2, and that the encoded protein was localized in the cell membrane. Sequence analysis of 102 modern Chinese rice varieties indicated that 3 variations at the LOC_Os06g06490 locus, among which C189G was proposed as a marker for indica-japonica differentiation, and A3259T which was specific to P50 might be as a functional variant. We hypothesize that mutations in the LOC_Os06g06490 locus affect the accumulation of indoleacetic acid, which regulates the length of young panicle. Therefore, the A3259T mutation may facilitate the breeding of better-quality high-yield japonica rice with moderate PL.