Genome-Wide Association Studies for Wheat Height Under Different Nitrogen Conditions

Lodging causes a reduction in wheat (Triticum aestivum L.) yield and quality. A shorter plant height (PH) can reduce the incidence of lodging. The overuse of nitrogen promotes excessive vegetative growth, leads to taller plants, and increases lodging risk. Here, we utilized genome-wide association studies (GWASs) to explore the genetic basis of PH and the nitrogen effect index (NEI), a parameter to estimate the responses of PH under varying nitrogen conditions, using 21,201 SNP markers from the Illumina Wheat 90K SNP array. A total of 191 wheat varieties from Yellow and Huai Valley regions of China, as well as other global regions, were analyzed across two growing seasons under four nitrogen treatments, namely N0 (0 kg/ha), N150 (150 kg/ha), N210 (210 kg/ha), and N270 (270 kg/ha). GWAS results showed that 30 genetic markers were associated with PH, explaining phenotypic variance from 5.92% to 13.69%. Additionally, nine significant loci were associated with the NEI. Notably, markers on chromosomes 1A and 6B were linked to both PH and the NEI, which were insensitive to low- and high-nitrogen fertilizers. In addition, the PH of the three cultivars (Zhoumai16, Zhoumai13, and Bima1) showed little variation in four nitrogen fertilizer levels. This study identified key genetic markers associated with wheat PH and the NEI, providing insights for optimizing nitrogen use in wheat breeding.