Objective The research explored the genetic mechanism for regulating chlorophyll content and its response to nitrogen (N) fertilizer in rice, and provide new molecular marker segments for breeding of high-yield and nitrogen- efficient rice varieties.

Method The 113 family lines of ZS 97 × MH 63 recombinant inbred lines (RIL, F₁₁) were adopted as tested materials for QTL analysis. Field experiments were performed with split-plot design, N fertilizer rate being the main plots and RIL being subplots. The low N (no N) and normal N (130, 135 N kg/hm²) fertilizer treatments were established in the fields. The chlorophyll meter was used to determine SPAD values of leaves at 30 days after transplanting (30 DAT) and at heading (HD) stage. By using a high-density genetic map containing 1 619 Bin markers, IciMappingv3.4 software and complete interval mapping, QTL for controlling leaf chlorophyll content at two growth stages was mapped.

Result In two N treatments at two growth stages within two years, a total of 15 QTLs for controlling leaf chlorophyll content were detected and they were located on chromosomes 1, 2, 3, 6, 7, 10 and 11. Each single QTL could explain 1.21%-40.74% of genetic contributions to traits. Through comparison of their physical loci, 6 QTLs were found to have been cloned or have the same loci being known previously for chlorophyll content. Among them, a locus, named qHDCHL6-1, regulating the chlorophyll content of flag leaf at heading stage was detected at 8.45-9.12Mb of chromosome 6. It was stably detected under two N treatments in two years, which explained 1.55%-28.01% of contributions to traits. Through functional annotation, 4 candidate genes related to chlorophyll content of flag leaf were found in the qHDCHL6-1 chromosome interval. These genes were LOC_Os06g15370 (OsNPF3.1), LOC_Os06g15420 (OsAS2), LOC_Os06g15620 (GAS) and LOC_Os06g15590, and the first three of these genes have been cloned

Conclusion 15 QTLs controlling leaf chlorophyll content of rice at 30 DAT and HD stage are detected, and a QTL locus qHDCHL6-1 with stable expression was identified, which contains 4 candidate genes.