Response of ZmPHO1 family members to low phosphorus stress and association of natural variation in ZmPHO1;2a reveal the role of low phosphorus tolerance

Phosphorus (Pi) is an essential nutrient for plants to sustain normal life processes. In this study, we found that the ZmPHO1 proteins had similar molecular weights and the same conserved domain. Phylogenetic and cis-acting element analysis showed that ZmPHO1s were divided into 4 subgroups, in which ZmPHO1;2a and ZmPHO1;2b were closely phylogenetic with OsPHO1;2b, and the promoter region of ZmPHO1s contained abundant abiotic stress-related elements. Quantitative real-time PCR (RT-qPCR) analyses showed that the expression of ZmPHO1s were induced under low-Pi stress, among ZmPHO1;2a and ZmPHO1;2b were up-regulated in 178 (low-Pi tolerance) roots. Further, pho1;2a mutant exhibited a reduction in Pi uptake, leading to decreased shoot biomass. Additionally, 196 single nucleotide polymorphism (SNPs) and 127 insertion-deletions (InDels) were detected in ZmPHO1;2a DNA region among the 278 inbred lines, and 14 natural variants were identified that were significantly associated with 14 phenotypic traits by using mixed linear model (MLM). Notably, we defined five haplotypes according to the variants that were significantly associated with low-Pi tolerance index and haplotype 2 can enhance biomass by promoting root diameter and volume. Similarly, 7 natural variants were detected in the promoter region of ZmPHO1;2a that were significantly associated with 18 phenotypic traits and included a pleiotropy variant (SNP-1302) whose allele G/G exhibited positive genetic effects on biomass. This study will provide a theoretical reference for further dissecting the molecular mechanism of ZmPHO1s regulating of the low-Pi stress response and contribute to the development of genetic markers.