Maize is one of the world’s most important food crops, yet environmental stresses such as high salinity and extreme temperatures can sharply reduce both its yield and grain quality. A new study published in BMC Genomics has taken a systematic, genome-wide look at one family of regulatory genes thought to sit behind many of the plant’s growth and stress responses: the SQUAMOSA PROMOTER BINDING PROTEIN–LIKE, or SPL, gene family. SPL genes encode a plant-specific class of transcription factors, proteins that switch other genes on or off, and are known from earlier work in plants to influence lateral branching, developmental phase transitions, flowering time and responses to stress. Until now, the authors report, a comprehensive characterization of the maize versions of these genes had not been carried out.
Working with the latest assembled B73 reference genome of maize, designated RefGen_v5 (Zm–B73–REFERENCE–NAM–5.0), the research team searched for SPL genes using sequence homology, the principle that related genes retain recognizable stretches of similar DNA sequence. The search identified 36 maize SPL genes, which the researchers named ZmSPLs. Mapping their positions revealed that the 36 genes are not spread evenly across the genome: instead, they display an uneven distribution pattern across all ten of maize’s chromosomes. That uneven layout is itself a clue to how the family has grown and been maintained over evolutionary time.
To organize the newly found genes, the team built a phylogenetic tree using maximum-likelihood analysis, a statistical method for inferring evolutionary relationships from sequence data. The analysis placed the 36 ZmSPLs into five distinct clades, or evolutionary branches, with significant variation in the number of genes belonging to each subgroup. When the researchers compared genes that fell into the same subclade, they found that these ZmSPLs shared highly conserved gene structures and protein motif architectures, meaning the layout of their coding regions and the functional building blocks of their proteins have been preserved across related members of the family.
The evolutionary history of the family also left measurable fingerprints. Collinearity analysis, which examines matching blocks of genes between chromosomes or between species, indicated that the ZmSPLs have undergone purifying selection during evolution, a process in which natural selection removes harmful mutations and keeps important gene functions intact. The analysis further pointed to segmental duplication, the duplication of large chromosome segments, as the primary driving force behind the expansion of the SPL family in maize. In addition, the ZmSPL genes showed conserved genomic correspondence with their counterparts in rice, suggesting that the arrangement of these genes has been largely preserved since the two species diverged.
Beyond gene sequences, the study examined the promoter regions of all 36 ZmSPLs, the stretches of DNA upstream of each gene that help control when and where it is switched on. These promoters contained a diverse set of regulatory elements: light-responsive elements, stress-responsive elements, hormone-responsive elements and development-related elements. The presence of such elements suggests that the genes are positioned to respond to a wide range of environmental and developmental cues, although promoter composition alone does not prove that any particular gene responds to a particular cue in living plants.
To connect the genomic predictions with actual gene activity, the researchers turned to expression data. They combined RNA-seq data, which measures gene activity across tissues, with RT-qPCR, a laboratory technique that quantifies the expression of specific target genes. This combined analysis showed that six of the ZmSPL genes, ZmSPL3, ZmSPL8, ZmSPL14, ZmSPL18, ZmSPL22 and ZmSPL30, are highly expressed in multiple tissues of the maize plant. More strikingly, the expression levels of these six genes were significantly induced or reduced in response to salinity and temperature stresses, indicating that their activity changes measurably when the plant is placed under these conditions.
The authors interpret these expression patterns as evidence that the six highlighted genes may play versatile roles in maize growth, development and stress response pathways, and they identify ZmSPL3/8/14/18/22/30 as prime targets for downstream functional investigation. The study is careful, however, to note the limits of what can currently be claimed: the specific biological functions of these genes remain to be experimentally validated. In other words, the work establishes where the genes sit in the genome, how they are related to one another and how their expression behaves under stress, but it does not yet demonstrate what each gene actually does in a growing maize plant.
Overall, the researchers describe their genome-wide characterization of the ZmSPLs as offering new perspectives on the family’s evolutionary dynamics and intergenic relationships. By cataloguing all 36 members in the newest reference genome, classifying them into five clades, tracing their duplication history and flagging the six most responsive members, the study provides a foundation that future functional studies can build on. For crop scientists interested in breeding maize varieties that hold their yield under salty soils or temperature extremes, the six stress-responsive ZmSPLs now stand out as the clearest starting points for the next round of experiments.
Subject of Research: Genome-wide identification and stress-response expression analysis of the SPL transcription factor gene family in maize
Article Title: Comprehensive identification, characterization, and stress response analysis of the ZmSPL gene family in maize (Zea mays L.)
Article References: Gu, L., Zhang, C., Chen, R., Nong, H., & Kang, T. (2026). Comprehensive identification, characterization, and stress response analysis of the ZmSPL gene family in maize (Zea mays L.). BMC Genomics. https://doi.org/10.1186/s12864-026-13536-7
Image Credits: AI Generated
DOI: 10.1186/s12864-026-13536-7
Keywords: maize, ZmSPL gene family, transcription factors, genome-wide identification, phylogenetics, segmental duplication, salinity stress, temperature stress, gene expression, RefGen_v5, BMC Genomics, Comprehensive
News Source: Juliet Wilcox. (November 7, 2026). Scientists Map 36 Maize SPL Genes Linked to Stress Responses. Scienmag.
