Fine Mapping and Functional Characterization of qKRN5.04b Reveals ZmGrx5 as a Domestication-Selected Regulator of Kernel Row Number in Maize

Kernel row number (KRN) is not only a key agronomic trait influencing maize yield but also a phenotype that underwent significant changes during maize domestication from its wild ancestor, teosinte. Previous studies have identified multiple quantitative trait loci (QTLs) associated with ear morphology on chromosome 5, among which the molecular basis and domestication role of qKRN5.04b remain unclear. To elucidate the function of qKRN5.04b, we constructed a segregating population through hybridization based on recombinant inbred lines derived from near-isogenic lines. Using high-throughput genotyping technologies and rigorously excluding interference from teosinte-derived chromosomal segments elsewhere in the genome, we narrowed the qKRN5.04b interval to a 3.8 Mb region. Transcriptomic analysis of immature maize ears revealed that differentially expressed genes were predominantly enriched in cis-regulatory RNA synthesis pathways, while KEGG pathway analysis indicated significant enrichment in auxin signal transduction. Functional validation showed that Mu insertion mutants of ZmGrx5 reduced kernel row number by two, suggesting ZmGrx5 as a candidate gene underlying qKRN5.04b. Population genetic analysis further demonstrated that ZmGrx5 is the most strongly selected member within the CC-type glutaredoxin (ROXY) family. Collectively, this study provides preliminary insights into the molecular basis of qKRN5.04b and offers valuable clues for understanding ROXY gene domestication and advancing molecular breeding strategies in maize. This study explores transcriptomic variation associated with inflorescence development and kernel row number (KRN) in maize using nearly isogenic recombinant inbred lines (NIRILs) derived from a cross between teosinte and maize. Specifically, two NIRILs, A12 and B46, differing in a defined introgressed segment on chromosome 5 from teosinte (Zea mays ssp. parviglumis), were selected for comparative analysis. Immature ears were collected at the V6–V9 leaf stages and manually dissected under a SZN71 Trinocular Macroscopic Co-visual Stereo Microscope (Soptop, Ningbo, China), selecting ear primordia measuring 1.5–2.0 mm staged between the inflorescence meristem (IM) and paired spikelet meristem (SPM). To ensure sample consistency, spikelets from at least 50 independently grown plants at the same developmental stage were pooled per biological replicate. Three biological replicates were collected for each genotype: M1, M2, and M4 from B46; T3, T5, and T6 from A12.The goal of this experiment was to identify genotype-specific transcriptional programs associated with early inflorescence patterning and KRN variation, thereby contributing to the understanding of domestication-related regulatory changes and informing future maize breeding strategies.