Integrating GWAS and Genomic Prediction to Breed Phosphorus-Efficient Bread Wheat

Phosphorus is a finite macronutrient involved in key metabolic activities in plants, therefore crops rely on soil P to grow and produce sufficient yield. However, the world's phosphorus resources in phosphate rocks are being exhausted. Breeding for tolerant bread wheat varieties towards P deficiency is becoming a pressing matter. In this study, a panel of 199 winter bread wheat genotypes were phenotyped in 2021 and 2022 in three trials in France and were genotyped using the TaBW280K SNP array, the 90K iSelect array and the 35K breeder chip. Trials were drilled in fields with low P concentrations, with and without added P. An agronomic characterization of the trials was conducted, measuring usual traits such as grain yield and earliness, as well as drone flights to follow several vegetation indices through time. P in the grains was quantified and traits related to P deficiency tolerance were calculated. The broad sense heritability of phosphorus use efficiency was 0.43 and interactions between genotypes and environments were analysed. We identified 17 quantitative trait loci (QTL) on 10 chromosomes (2A, 2B, 2D, 3A, 4B, 4D, 5A, 5B, 6B and 7B) through a genome-wide association study (GWAS) for traits related to tolerance to P deficiency. Some of the QTLs found in this study colocalized with known genes. Genomic prediction models were built to evaluate their possible use in the early breeding stages for Phosphorus deficiency tolerance.