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Optimising nitrogen fertiliser management in combination with using high nitrogen efficient wheat cultivars is the most effective strategy to maximise productivity in a cost-efficient manner. The present study was designed to investigate the associations between nitrogen utilisation efficiency (NUtE) and the allelic composition of the NAM genes in Australian wheat cultivars. As results, the non-functional NAM-B1 allele was more responsive to the nitrogen levels and increased NUtE significantly, leading to a higher grain yield but reduced grain protein content. Nitrogen application at different developmental stages (mid-tillering, booting, and flowering) did not show significant differences in grain yield and protein content. The NAM-A1 allelic variation is significantly associated with the length of the grain-filling period. While the NAM-A1 allele a was associated with a short to moderate grain-filling phase, the alleles c and d were related to moderate to long grain-filling phase. Thus, selection of appropriate combinations of NAM gene alleles can fine-tune the duration of growth phases affecting sink-source relationships which offers an opportunity to develop high NUtE cultivars for target environments.

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In the present study, four large-scale field trials using two doubled haploid wheat populations were conducted in different environments for two years. Grain protein content (GPC) and 21 other yield-related traits were investigated. A total of 227 QTL were mapped on 18 chromosomes, which formed 35 QTL clusters. The potential candidate genes underlying the QTL clusters were suggested. Furthermore, adding to the significant correlations between yield and its related traits, correlation variations were clearly shown within the QTL clusters. The QTL clusters with consistently positive correlations were suggested to be directly utilized in wheat breeding, including 1B.2, 2A.2, 2B (4.9–16.5 Mb), 2B.3, 3B (68.9–214.5 Mb), 4A.2, 4B.2, 4D, 5A.1, 5A.2, 5B.1, and 5D. The QTL clusters with negative alignments between traits may also have potential value for yield or GPC improvement in specific environments, including 1A.1, 2B.1, 1B.3, 5A.3, 5B.2 (612.1–613.6 Mb), 7A.1, 7A.2, 7B.1, and 7B.2. One GPC QTL (5B.2: 671.3–672.9 Mb) contributed by cultivar Spitfire was positively associated with nitrogen use efficiency or grain protein yield and is highly recommended for breeding use. Another GPC QTL without negatively pleiotropic effects on 2A (50.0–56.3 Mb), 2D, 4D, and 6B is suggested for quality wheat breeding.