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Studying the regulatory mechanisms that drive nitrogen-use efficiency (NUE) in crops is important for sustainable agriculture and environmental protection. In this study, we generated a high-quality genome assembly for the high-NUE wheat cultivar Kenong 9204 and systematically analyzed genes related to nitrogen uptake and metabolism. By comparative analyses, we found that the high-affinity nitrate transporter gene family had expanded in Triticeae. Further studies showed that subsequent functional differentiation endowed the expanded family members with saline inducibility, providing a genetic basis for improving the adaptability of wheat to nitrogen deficiency in various habitats. To explore the genetic and molecular mechanisms of high NUE, we compared genomic and transcriptomic data from the high-NUE cultivar Kenong 9204 (KN9204) and the low-NUE cultivar Jing 411 and quantified their nitrogen accumulation under high- and low-nitrogen conditions. Compared with Jing 411, KN9204 absorbed significantly more nitrogen at the reproductive stage after shooting and accumulated it in the shoots and seeds. Transcriptome data analysis revealed that nitrogen deficiency clearly suppressed the expression of genes related to cell division in the young spike of Jing 411, whereas this suppression of gene expression was much lower in KN9204. In addition, KN9204 maintained relatively high expression of NPF genes for a longer time than Jing 411 during seed maturity. Physiological and transcriptome data revealed that KN9204 was more tolerant of nitrogen deficiency than Jing 411, especially at the reproductive stage. The high NUE of KN9204 is an integrated effect controlled at different levels. Taken together, our data provide new insights into the molecular mechanisms of NUE and important gene resources for improving wheat cultivars with a higher NUE trait. A high-quality genome assembly of the high-NUE wheat cultivar Kenong 9204 was generated and genes related to nitrogen uptake and metabolism were systematically analyzed. Genomic and transcriptomic comparative analyses of Kenong 9204 with the low-NUE cultivar Jing 411 revealed key developmental stages and associated metabolic pathways responsible for N status, as well as possible molecular mechanisms that drive NUE in wheat. [ABSTRACT FROM AUTHOR]

Summary: Hybrid necrosis, caused by complementary genes Ne1 and Ne2, is a serious barrier for combining desirable traits from different genotypes of wheat, affecting the full utilisation of heterosis. To date, both Ne1 and Ne2 are still not isolated although they were documented decades ago.We report here the map‐based cloning and functional characterisation of Ne2, encoding a coiled coil–nucleotide‐binding site–leucine‐rich repeat (CC–NBS–LRR) protein. Homozygous frameshift mutations generated using the CRISPR/Cas9 approach confirmed the Ne2‐inducing hybrid necrosis in wheat. Upregulated expression of Ne2 induced by Ne1 and excess hydrogen peroxide accumulation are associated with the necrosis formation.Genetic analyses of a Ne2 allele (Ne2m) and leaf rust resistance gene LrLC10/Lr13 revealed that they might be the same gene. Furthermore, we demonstrated that the frequency of the Ne2 allele was much lower in landraces (2.00%) compared with that in modern cultivars (13.62%), suggesting that Ne2 allele has been partially applied in wheat genetic improvement.Our findings open opportunities of thoroughly investigating the molecular mechanism of hybrid necrosis, selecting Lr13 and simultaneously avoiding hybrid necrosis in wheat breeding through marker‐assisted selection. [ABSTRACT FROM AUTHOR]