Identification and fine mapping of qTGW11, a QTL conferring high nitrogen use efficiency in Dongxiang wild rice (Oryza rufipogon Griff.)

Yumin Shen; Wentao Xiong; Aiping Shu; Lanxiang Hu; Shiyou Luo; Jintao Huang; Huanjin Xiong; Xiaoyan Wu; Yeqing Xiao; Mingliang Chen

doi:10.1016/j.jplph.2025.154562

Identification and fine mapping of qTGW11, a QTL conferring high nitrogen use efficiency in Dongxiang wild rice (Oryza rufipogon Griff.)

J Plant Physiol. 2025 Jul 5:312:154562. doi: 10.1016/j.jplph.2025.154562. Online ahead of print.

Authors

Affiliations

¹ Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang, Jiangxi, 330200, China; Nanchang Branch of Chinese National Center for Rice Improvement, Nanchang, Jiangxi, 330200, China; National Engineering Research Center of Rice, Nanchang, Jiangxi, 330200, China.
² Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang, Jiangxi, 330200, China.
³ Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang, Jiangxi, 330200, China. Electronic address: cml82@163.com.

PMID: 40652677
DOI: 10.1016/j.jplph.2025.154562

Abstract

The extensive utilization of synthetic nitrogen fertilizers has substantially increased crop yields while severely disrupting the ecological balance. Consequently, enhancing nitrogen use efficiency in crops has become imperative for sustainable agricultural development. Dongxiang wild rice (DXWR), demonstrating remarkable tolerance to low-nitrogen stress, represents a precious germplasm resource for breeding nitrogen-efficient rice cultivars. In this study, we conducted quantitative trait loci (QTL) mapping for plant height, effective panicle number, grain number per panicle, grain yield per plant, and thousand-grain weight under low-nitrogen and normal-nitrogen conditions using 150 backcross recombinant inbred lines (BILs) derived from a cross between the indica maintainer line GanxiangB and DXWR, with a genetic linkage map comprising 153 SSR markers. Of 23 QTLs identified across 11 chromosomes, 9 were consistently detected under both nitrogen conditions. A stable QTL qTGW11 was identified under both nitrogen conditions; explaining 8.37-9.57 % of the phenotypic variation. Through map-based cloning, qTGW11 was precisely localized to a 117-kb genomic region harboring 16 candidate genes, among which LOC_Os11g40100 was identified as the most likely causal gene through quantitative reverse transcription PCR (qRT-PCR) validation.

Keywords: Dongxiang wild rice; Mapping; Nitrogen use efficiency; QTL; qTGW11.