QTL analysis of panicle neck diameter, a trait highly correlated with panicle size, under well-watered and drought conditions in rice (Oryza sativa L.)

The panicle neck diameter was measured in a rice population of 187 lines from the cross “‘ZS97B’/‘IRAT109”’ under water regimes in 2003 and 2004. PND was found to be significantly correlated with many agronomical traits, especially with the panicle size. Based on a linkage group of 213 SSR markers, totally three main effect QTLs were detected for PND with contribution rates varying from 5.03% to 11.01%, including one locus detected under both water conditions (qPND-4). The chromosomal region on chromosome 4 (RM241-Rm349) also hosted QTLs for seven panicle traits, including panicle number, panicle length, primary branch number, secondary branch number, spikelet number per panicle, spikelet density and grain number per panicle. Seventeen epistatic QTLs were detected for PND under well-watered and stress conditions. The contribution rate of each pair of epistatic effect varied from 2.58% to 5.64%.