Cloning and expression analysis of candidate genes. A) Identification of P efficiency candidate gene by combining linkage mapping and GWAS. B) Candidate gene haplotypes in the 219-accession panel. C) Natural variations of the candidate gene were associated with low P tolerance in 219 soybean accessions. Analysis of relative plant height of 6 haplotypes (Hap1, n = 109; Hap2, n = 85; Hap3, n = 9; Hap4, n = 7; Hap5, n = 5; Hap6, n = 4) in the 219-accession panel. For all boxplots, center line, median; box limits, upper, and lower quartiles; whiskers, 1.5 × interquartile range; points, outliers. D) Candidate gene (GmRR1) expression analyses in various organs of soybean Nannong94-156, including roots, stems, leaves, flowers, 15d pods, 45d pods, 15d seeds, and 45d seeds. Data are means ± standard error of the mean (n = 3). E) Analysis of relative expression of GmRR1 in transgenic plants and mutants (n = 3). ko-1, ko-2, and ko-3 represent three different knockout lines; OE-1 OE-2, and OE-3 represent three different overexpression lines. Significant differences compared to WT according to two-sided t test (***P < 0.001). Data are means ± standard error of the mean (n = 3).