Unveiling novel QTLs for nitrogen use efficiency in temperate Japonica rice

Nitrogen (N) is essential for rice growth and has driven yield increases since the 1950s. However, excessive use of mineral N fertilizers has led to considerable environmental and economic concerns. Enhancing nitrogen use efficiency (NUE) is essential for reducing these impacts and ensuring global food security. Decades of breeding under high N application have reduced the fertilizer responsiveness of modern temperate japonica rice varieties, further contributing to NUE inefficiencies. This study aimed to uncover the genetic components underlaying NUE in temperate-adapted japonica rice varieties.

A genome-wide association study (GWAS) with PCA and kinship matrix was conducted on a panel of 153 temperate japonica rice accessions using 97,244 single-nucleotide polymorphisms (SNPs) to detect quantitative trait loci (QTLs) for NUE. Phenotypic evaluations were conducted under two distinct nitrogen levels across three different field environments. Significant influences of both nitrogen level and environment were observed on trait expression. A total of 14 marker trait associations (MTAs) were identified and grouped into eight QTLs. Within these regions 350 genes were identified and among them three candidate genes were pinpointed including a gene involved in N uptake and transport (OsNAR2.1) and two transcription factors related to N use and metabolism or regulated by the N availability (OsARF19 and OsMADS27). In addition, three novel loci associated with enhanced NUE (chr02:22969295, chr01:33259076, and chr09:17345345) emerged as promising targets for marker-assisted selection. A phylogenetic analysis of the allele distribution for the candidate genes across the collection revealed significant variation in NUE among the genetic clusters, with one cluster exhibiting superior NUE performance under the tested conditions highlighting the genetic components of NUE.

This study provides genetic insights into NUE in temperate japonica rice. We have identified QTLs associated with NUE traits, some of which co-localized with previously identified genes, while also providing novel molecular markers. The identified loci and candidate genes offer valuable genetic resources to support molecular breeding strategies aimed at improving NUE in japonica rice cultivars adapted to temperate climates.