Genome-wide association study and BSR-seq identify nitrate reductase-related genes in rice landraces (Oryza sativa...

Nitrogen (N) is an essential nutrient for rice (Oryza sativa L.) growth and development. However, the lower nitrogen use efficiency (NUE) results in an N fertilizer surplus, which causes many environmental problems. In this study, genome-wide association studies were used to detect nitrate reductase (NR)-related loci in 419 rice landraces. Using the general linear model (GLM), mixed linear model (MLM), linear model (LM), and linear mixed model (LMM), we found six, nine, seven, and six significant single-nucleotide polymorphisms (SNPs) associated (p < 1 × 10^-5) for three traits. Moreover, 98 significant SNPs were associated (logarithm of odds ≥ 3) with three traits through 3 V multi-locus random-SNP-effect mixed linear model. Interestingly, we found that Chr1_15896481 was significantly associated in the GLM, MLM, LM, and LMM models. Meanwhile, this significant locus overlapped with a candidate region in bulked segregant RNA sequencing. Through integrated analysis, we identified a most likely candidate genomic region 15,627,420-16,084,761 bp on chromosome 1. By performing functional annotation, RNA sequencing, and real-time quantitative polymerase chain reaction (RT-qPCR) analysis for the genes within this interval, we identified five candidate genes that may affect NR activity. Os01g0378400 exhibits a gene expression pattern highly similar to that of OsNR1.2. It belongs to the NAC transcription factor family, which is involved in plant N metabolism. Os01g0377700 is homologous to an ammonium transporter gene (Cre06g293051). Os01g0383700 encodes a WD40 domain protein, Os01g0379400 encodes an F-box protein, and Os01g0382800 encodes a DYW-type PPR domain protein. These findings will provide valuable genetic resources for NUE genetic improvement in rice breeding.