High-throughput root phenotyping and association analysis identified potential genomic regions for phosphorus use efficiency in wheat (Triticum aestivum L.).

Main conclusion: Association analysis identified 77 marker-trait associations (MTAs) for PUE traits, of which 10 were high-confidence MTAs. Candidate-gene mining and in-silico expression analysis identified 13 putative candidate genes for PUE traits. Bread wheat (Triticum aestivum L.) is a major cereal crop affected by phosphorus (P) deficiency, which affects root characteristics, plant biomass, and other attributes related to P-use efficiency (PUE). Understanding the genetic mechanisms of PUE traits helps in developing bread wheat cultivars that perform well in low-P environments. With this objective, we evaluated a bread wheat panel comprising 304 accessions for 14 PUE traits with high-throughput phenotyping under low-P and optimum-P treatments and observed a significant genetic variation among germplasm lines for studied traits. Genome-wide association study (GWAS) using 14,025 high-quality single-nucleotide polymorphisms identified 77 marker-trait associations (MTAs), of which 10 were chosen as high-confidence MTAs as they had > 10% phenotypic variation with logarithm of odds (LOD) scores of more than five. Candidate-gene (CG) mining from high-confidence MTAs identified 180 unique gene models, of which 78 were differentially expressed (DEGs) with at least twofold change in expression under low-P over optimum-P. Of the 78-DEGs, 13 were thought to be putative CGs as they exhibited functional relevance to PUE traits. These CGs mainly encode for important proteins and their products involved in regulating root system architecture, P uptake, transport, and utilization. Promoter analysis from 1500 bp upstream of gene start site for 13 putative CGs revealed the presence of light responsive, salicylic-acid responsive, gibberellic-acid (GA)-responsive, auxin-responsive, and cold responsive cis-regulatory elements. High-confidence MTAs and putative CGs identified in this study can be employed in breeding programs to improve PUE traits in bread wheat.