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.