Objectives Phosphorus (P) is one of the essential nutrients for rice growth, and insufficient phosphorus supply will affect rice yield and quality. We studied the physiological response and differential expression of genes in rice roots to low phosphorus conditions, aiming to serve the selection and breeding of rice varieties with efficient phosphorus absorption and utilization in agricultural production.

Methods A phosphorus sensitive genotype Tongjing 981 (TJ981), a low phosphorus tolerant genotype Zhenghan 6 (ZH6), and a root extension type Zhendao 99 (ZD99) were selected as the research materials in a hydroponic experiment. Normal and low phosphorous nutrition solution was prepared as control (CK) and low P treatment (LP), the P concentration in LP solution was 5% of that in +P solution. At 1, 8, and 15 days of treatment, rice seedlings were sampled for measurement. The differentially expressed genes (DEGs) were analyzed using transcriptome sequencing (RNA seq) technology, protein mass spectrometry analysis, and real-time fluorescence quantitative PCR (RT-PCR) technology; the root phosphorus content and acid phosphatase (APase) activity, and rhizosphere pH were measured at the same time.

Results LP treatment increased the number of DEGs on the roots of all the three rice varieties, the up- and down-regulated DEGs were 447 and 1395 for Tongjing 981, 352 and 1185 for Zhendao 99, and 475 and 1856 for Zhenghan 6, respectively. There were a total of 237 DEGs that identified in all the three varieties, of them, 33 were upregulated and 204 were downregulated. The P contents in the roots of rice variety Tongjing 981, Zhendao 99, and Zhenghan 6 under LP condition were 41.31%, 36.29%, and 33.17% of those under +P condition, the decrease exceeded the P concentration gap between the two culture solutions, indicating that the upregulation of the expression of the inorganic phosphorus transporter 1-2 gene promoted the absorption of phosphorus by roots. At the 1, 8, and 15 days of LP treatment, the activity of APase of three rice varieties were all higher than those of +P, which could be explained by the variation of the differential expression of the purple acid phosphatase gene.

Conclusions The number of superimposed inhibited genes was significantly higher than that of induced genes, that is, the number of down-regulated genes was much more than that of up-regulated genes. By inducing the expression of inorganic phosphorus transporter OsPT1-2 in rice roots, the uptake of available phosphorus in low-phosphorus rice roots was promoted. By inducing the expression of purple acid phosphatase and plasma membrane H⁺-ATpase genes in rice roots, the activity of acid phosphatase secreted by rice roots increased, and H⁺ transport and secretion led to a decrease in rhizosphere pH, thus promoting the activation of organic and inorganic binding phosphorus and improving the efficient utilization of phosphorus.