A natural uORF variant confers phosphorus acquisition diversity in soybean

Phosphorus (P) is an essential element for all organisms. Because P fertilizers are a non-renewable resource and P is highly fixed in soils, sustainable agriculture requires improving crop P acquisition efficiency. Here, a strong association signal at a locus named CPU1 (component of phosphorus uptake 1) was identified by genome-wide association study (GWAS) of P acquisition efficiency in a soybean core collection grown in the field. A SEC12-like gene, GmPHF1, was identified as the causal gene for CPU1. GmPHF1 facilitates endoplasmic reticulum (ER) exit of the phosphate transporter GmPT4 to the plasma membrane of root epidermal cells. A common SNP in an upstream open reading frame (uORF) of GmPHF1 alters GmPHF1 abundance in a tissue-specific manner and contributes to P acquisition diversity in soybean. This natural genetic variation can be used to develop P-efficient soybean genotypes.