Although several pentatricopeptide repeat (PPR) proteins are involved in post-transcriptional processing of mitochondrial RNA, it is unclear which specific protein is involved in the RNA editing of ccmC in maize (Zea mays). Here we report the identification of the maize empty pericarp 601 (emp601) mutant and the map-based cloning of the Emp601 gene, which encodes an E2-type PPR protein that is targeted to mitochondria. A single-nucleotide deletion in the emp601 mutant caused a frameshift and introduced a premature stop codon into the predicted EMP601. This mutation was associated with reduced accumulation of mitochondrial complex Ⅲ as well as with inhibition of growth and differentiation of basal endosperm transfer layer cells, leading to final degeneration of the embryo and endosperm. We determine that loss of EMP601 function prevents the C-to-U RNA editing of the mitochondrial transcript ccmC at position 358. EMP601 binds to the ccmC transcript and directly interacts with Multiple organellar RNA editing factor 8 and may be a component of the plant mitochondrial editosome. We conclude that EMP601 functions in RNA editing of mitochondrial ccmC transcripts and influences mitochondrial function and seed development.

Gene resources associated with plant stature and flowering time are invaluable for maize breeding. In this study, using an F_2:3 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.

Drought is one of the most critical abiotic stresses influencing maize yield. Improving maize cultivars with drought tolerance using marker-assisted selection requires a better understanding of its genetic basis. In this study, a doubled haploid (DH) population consisting of 217 lines was created by crossing the inbred lines Han 21 (drought-tolerant) and Ye 478 (drought-sensitive). The population was genotyped with a 6 K SNP assay and 756 SNP (single nucleotide polymorphism) markers were used to construct a linkage map with a length of 1344 cM. Grain yield (GY), ear setting percentage (ESP), and anthesis–silking interval (ASI) were recorded in seven environments under well-watered (WW) and water-stressed (WS) regimes. High phenotypic variation was observed for all traits under both water regimes. Using the LSMEAN (least-squares mean) values from all environments for each trait, 18 QTL were detected, with 9 associated with the WW and 9 with the WS regime. Four chromosome regions, Chr. 3: 219.8–223.7 Mb, Chr. 5: 191.5–194.7 Mb, Chr. 7: 132.2–135.6 Mb, and Chr. 10: 88.2–89.4 Mb, harbored at least 2 QTL in each region, and QTL co-located in a region inherited favorable alleles from the same parent. A set of 64 drought-tolerant BC₃F₆ lines showed preferential accumulation of the favorable alleles in these four regions, supporting an association between the four regions and maize drought tolerance. QTL-by-environment interaction analysis revealed 28 edQTL (environment-dependent QTL) associated with the WS regime and 22 associated with the WW regime for GY, ESP, and ASI. All WS QTL and 55.6% of WW QTL were located in the edQTL regions. The hotspot genomic regions identified in this work will support further fine mapping and marker-assisted breeding of drought-tolerant maize.