Identification of ZmPH1 as a plant height novel gene in maize

Plant height is a key agricultural trait for lodging resistance in maize. To explore key genes regulating plant height, a genome-wide association study (GWAS) was conducted using a large population of 1149 inbred lines. Plant height (PH), ear height (EH), and ear height coefficient (EH/PH) in this population followed a standard normal distribution, with heritability of 86%, 85%, and 75%, respectively. The GWAS identified two significant SNPs (Chr3:163963128 and Chr3:163963155) associated with all three traits. Within a 100-kb genomic region spanning upstream and downstream of the two SNPs, four genes were examined by real-time PCR, and among them, ZmPH1 showed a significant difference between taller lines and shorter lines. ZmPH1 encodes a pentatricopeptide repeat protein. ZmPH1 was also found to colocalize with a mapped PH QTL (qPH3-1) and an EH QTL (qEH3-1) identified in our F₂ mapping population. The inbred lines were classified into Hap1 and Hap2 based on the genotype of ZmPH1. Hap1 lines have significantly taller PH and EH than Hap2 lines. A KASP marker designed based on one SNP successfully distinguished tall and short inbred lines after PCR amplification. Subcellular localization analysis showed that ZmPH1 is a chloroplast-localized protein. This study presents a potential PPR gene involved in the regulation of plant height and provides potential genetic resources for maize plant height breeding.