The Acid Phosphatase-Encoding Gene <i>GmACP1</i> Contributes to Soybean Tolerance to Low-Phosphorus Stress

<div><p>Phosphorus (P) is essential for all living cells and organisms, and low-P stress is a major factor constraining plant growth and yield worldwide. In plants, P efficiency is a complex quantitative trait involving multiple genes, and the mechanisms underlying P efficiency are largely unknown. Combining linkage analysis, genome-wide and candidate-gene association analyses, and plant transformation, we identified a soybean gene related to P efficiency, determined its favorable haplotypes and developed valuable functional markers. First, six major genomic regions associated with P efficiency were detected by performing genome-wide associations (GWAs) in various environments. A highly significant region located on chromosome 8, <i>qPE8</i>, was identified by both GWAs and linkage mapping and explained 41% of the phenotypic variation. Then, a regional mapping study was performed with 40 surrounding markers in 192 diverse soybean accessions. A strongly associated haplotype (<i>P</i> = 10⁻⁷) consisting of the markers Sat_233 and BARC-039899-07603 was identified, and <i>qPE8</i> was located in a region of approximately 250 kb, which contained a candidate gene <i>GmACP1</i> that encoded an acid phosphatase. <i>GmACP1</i> overexpression in soybean hairy roots increased P efficiency by 11–20% relative to the control. A candidate-gene association analysis indicated that six natural <i>GmACP1</i> polymorphisms explained 33% of the phenotypic variation. The favorable alleles and haplotypes of <i>GmACP1</i> associated with increased transcript expression correlated with higher enzyme activity. The discovery of the optimal haplotype of <i>GmACP1</i> will now enable the accurate selection of soybeans with higher P efficiencies and improve our understanding of the molecular mechanisms underlying P efficiency in plants.</p>