Identification of Candidate Genes for Low Phosphorus Tolerance in Maize Seedling Stage Based on GWAS and Transcriptome.

Phosphorus is an essential nutrient for maize growth and development, and its deficiency can significantly inhibit plant growth, leading to reduced yield and quality. To elucidate the genetic mechanisms underlying low phosphorus tolerance in maize, this study utilized a panel of 257 maize inbred lines and conducted controlled experiments under low phosphorus (LP) and normal phosphorus (CK) conditions in artificial climate chambers. Through genome-wide association study (GWAS), a total of 46 SNP loci significantly associated with low phosphorus tolerance were detected, and 74 candidate genes were predicted. To further investigate, the low-phosphorus tolerant material CML422 and the phosphorus-sensitive material CIMBL90 were selected for transcriptome sequencing, which identified a total of 7232 differentially expressed genes (DEGs). KEGG enrichment analysis revealed that these genes were significantly enriched in key pathways such as plant hormone signal transduction, MAPK signaling pathway, and starch and sucrose metabolism, suggesting that maize responds to low phosphorus stress through the coordinated regulation of multiple pathways. By integrating GWAS and transcriptome data, 18 co-localized genes were screened, ultimately identifying 10 candidate genes closely associated with low phosphorus tolerance during the maize seedling stage, which are potentially involved in regulating growth and development under phosphorus stress. This study preliminarily elucidates the molecular mechanisms underlying low phosphorus tolerance in maize through multi-omics analysis, providing both a theoretical basis and genetic resources for breeding new maize varieties with high phosphorus use efficiency.