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 desirable for sustainable agriculture. Genetic dissection and identification of causative genes for nutrient use efficiency is the ideal strategy to achieve this goal. We conducted an extensive genome-wide association study (GWAS) employing a panel of 431 genotyped wheat cultivars, revealing 1659 significant single-nucleotide polymorphisms (SNPs) (LOD>5) via genotyping-by-sequencing. Our investigation uncovered 534 quantitative trait loci (QTLs) associated with 12 nutrient use efficiency traits across five distinct environments, of which 14 QTLs were consistently identified in at least three environments. Through the integration of meta-QTL analysis, it is noteworthy that QTL80 (72.12-74.24 Mb, chr2A), QTL387 (32.88-33.56 Mb, chr6A), and QTL500 (535.53-540.80 Mb, chr7B) manifest a distinct co-localization with MQTL-2A-2, MQTL-6A-1, and MQTL-7B-2, respectively. This convergence underscores their substantive relevance across a spectrum of diverse environmental conditions. Within these regions, pivotal candidate genes, such as the bZIP transcription factor family gene and potassium transporter gene, associated with nutrient use efficiency were discerned. Furthermore, a novel locus, QTL234, emerged, housing key candidate genes like dof zinc finger protein, Ankyrin repeat family protein, and cytochrome P450. To validate the SNP located within QTL234 associated with nitrogen harvest index (NHI), we developed a dCAPS marker for AX-109095537. These findings underscore the efficacy of high-resolution SNP-based GWAS in swiftly identifying potential key candidate genes. Additionally, they solidify the groundwork for large-scale QTL fine mapping, candidate gene validation, and the development of functional markers crucial for advancing nutrient use efficiency breeding in wheat.