Analysis of flowering time network function of tropical and temperate maize

Abstract

The floral transition in maize is a key developmental switch from vegetative to reproductive growth. Its timing is shaped by internal cues and external signals such as photoperiod and strongly influences flowering time, a crucial adaptive trait under selection. Maize varieties adapted to temperate latitudes exhibit photoperiod insensitivity and flower consistently under both short (SD) and long (LD) day conditions, whereas tropical maize, retaining much of the photoperiod sensitivity of its teosinte progenitor, requires SD to flower within a similar timeframe as temperate maize. The switch in photoperiod sensing and response is not well understood, particularly in plants adapted to SD environments. We still lack a clear picture of how developmental programs were rewired as SD tropical maize adapted to LD temperate regions. To address this knowledge gap, this work aims to clarify the phenotypic responses and molecular mechanisms that differentiate photoperiod sensitive from insensitive maize. We conducted four years of field-based phenotyping of temperate (B73, B104, Mo17) and tropical (CML10, CML277, CML258, Tzi8, Tzi9) maize inbreds under SD and LD. The quantification of the degree of photoperiod sensitivity for each genotype establishes a baseline for comparisons with genome-edited lines to evaluate their response to specific gene edits. We used this baseline to assess the effects of editing key flowering repressors on flowering traits of a tropical inbred grown under SD and LD conditions, demonstrating our success in generating earlier flowering Tzi8 lines whose flowering time now partially overlaps with that of temperate lines under LD. These edited lines are suitable for temperate breeding programs and have the potential to help recover lost tropical genetic diversity. We analyzed transcriptome wide expression patterns over a daily cycle at two developmental stages (before and after the floral transition) in a tropical line and one stage in a temperate line grown under SD, identifying rhythmic genes in all conditions. After the floral transition, the two genotypes share a core enriched for functions related to organelle maintenance and gene-expression capacity, alongside genotype-specific functions. Core circadian and light-signaling genes remained active, while their co-expression partners and phases shifted with stage and genotype. In Tzi8, vegetative stage rhythmic enrichment prioritizes building translational machinery and energy production, whereas reproductive stage shifts toward regulatory sophistication with attenuated translation-related terms. We also provided a needed detailed protocol for Chromatin Immunoprecipitation (ChIP) method. Together, this research advances understanding of photoperiod adaptation in maize and supports long-term efforts to accelerate maize genetic improvement, either by incorporating the edited lines as a new source of genetic diversity or by targeting key floral transition genes using gene-editing technologies.