Genome-wide association study reveals genomic regions for nitrogen, phosphorus and potassium use efficiency in bread wheat

The development of wheat cultivars with improved nitrogen (N), phosphorus (P), and potassium (K) use efficiency is essential for sustainable agriculture. Genetic dissection and identification of causative genes underlying nutrient use efficiency represent a key strategy toward this goal. We conducted an extensive genome-wide association study (GWAS) using a panel of 431 wheat cultivars, identifying 1,659 significant single-nucleotide polymorphisms (SNPs) (LOD>5) through genotyping-by-sequencing. This analysis revealed 534 quantitative trait loci (QTLs) associated with 12 nutrient use efficiency traits across five distinct environments, among which 14 QTLs were consistently detected in at least three environments. Notably, meta-QTL analysis, showed that QTL80 (72.12–74.24 Mb, chr2A), QTL387 (32.88–33.56 Mb, chr6A), and QTL500 (535.53–540.80 Mb, chr7B) exhibit clear co-localization with MQTL-2A-2, MQTL-6A-1, and MQTL-7B-2, respectively. This overlap highlights their robustness across diverse environmental conditions. Within these regions, critical candidate genes – including members of the bZIP transcription factor family and a potassium transporter gene – were identified in relation to nutrient use efficiency. Furthermore, a novel locus, QTL234, was discovered, harboring key candidate genes such as dof zinc finger protein, Ankyrin repeat family protein, and cytochrome P450. To validate the SNP within QTL234 associated with nitrogen harvest index (NHI), we developed a dCAPS marker for AX-109095537. These findings demonstrate the effectiveness of high-resolution SNP-based GWAS in rapidly pinpointing promising candidate genes. They also establish a foundation for large-scale QTL fine mapping, candidate gene validation, and the development of functional markers essential for enhancing nutrient use efficiency in wheat breeding programs.