Cloning of a new allele of ZmAMP1 and evaluation of its breeding value in hybrid maize

Gene resources associated with plant stature and flowering time are invaluable for maize breeding. In this study, using an F2:3 population derived from a natural semi-dwarf mutant grmm and a normal inbred line Si 273, we identified a major pleiotropic QTL on the distal long arm of chromosome 1 (qPH1_dla), and found that qPH1_dla controlled plant height, flowering time, ear and yield traits. qPH1_dla was fine-mapped to a 16 kb interval containing ZmAMP1, which was annotated as a glutamate carboxypeptidase. Allelism tests using two independent allelic mutants confirmed that ZmAMP1 was the causal gene. Real-time quantitative PCR and genomic sequence analysis suggested that a nonsynonymous mutation at the 598th base of ZmAMP1 gene was the causal sequence variant for the dwarfism of grmm. This novel ZmAMP1 allele was named ZmAMP1_grmm. RNA sequencing using two pairs of near isogenic lines (NILs) showed that 84 up-regulated and 68 down-regulated genes in dwarf NILs were enriched in 15 metabolic pathways. Finally, introgression of ZmAMP1_grmm into Zhengdan 958 and Xianyu 335 generated two improved F1 lines. In field tests, they were semi-dwarf, early-flowering, lodging-resistant, and high-yielding under high-density planting conditions, suggesting that ZmAMP1_grmm is a promising Green Revolution gene for maize hybrid breeding.