Enhancing nitrogen-use efficiency (NUE) in crops is crucial for sustainable agriculture, as it reduces the need for synthetic nitrogen fertilizers, which are both costly and environmentally damaging. Efficient nitrogen use improves crop yields and stability under varying environmental conditions. This is particularly important for wheat, which is grown on more than 240 million hectares globally, as improvements in NUE can significantly impact overall nitrogen consumption.

In this study, we employed a multi-pronged approach to explore genetic variation for NUE in wild wheat Aegilops tauschii, the D-genome donor of common wheat. A panel of 135 Ae. tauschii accessions, sequenced under the Open Wild Wheat Consortium, was evaluated for root architecture and agromorphological traits under two nitrogen levels. Association mapping using 36,373,307 SNP markers identified 69 and 51 marker-trait associations for traits under N60 and N120 conditions, respectively.

Expression profiling of the putative candidate genes provided valuable insights for enhancing NUE through marker-assisted selection in wheat breeding programs using Ae. tauschii accessions with high NUE. A second strategy involved mining genetic variations for NUE in backcross introgression line libraries (BILs) derived from two in-house developed synthetic wheats. These BILs were phenotyped for NUE and yield traits at three differential nitrogen levels in two environments. The libraries were genotyped with 9,474 SNP markers using the 35K Axiom® Wheat Breeder’s Array. Significant phenotypic variation was observed across 22 traits, and 65 marker-trait associations (MTAs) were identified, linked to various biological processes and yield traits.

Nitrate transporters are key genes for nitrogen metabolism, especially in cereal crops, due to the significant costs associated with nitrogen fertilizers. Four nitrate transporter gene families are known: NPF, NRT2, CLC, and SLAC/SLAH. In silico analysis identified 20 root-specific, 11 leaf/shoot-specific, and 17 grain/spike-specific genes in the hexaploid wheat genome. These genes were collocated to marker-trait associations related to nitrogen use efficiency identified in previous studies. However, the diversity of nitrate transporter (NRT2) genes in wild species is less understood. Novel allelic variations in 18 NRT2 genes were also mined from the genome of 306 Ae. tauschii accessions, identifying an average of 15 SNPs per gene, including those causing missense mutations or stop codons. Four to six haplotypes for these genes were generated and are being correlated with NUE.

These findings from multiple studies offer promising avenues for developing nitrogen-efficient, high-yielding wheat varieties by utilizing selected donors and the NUE-associated genes/alleles identified in this research.