Genome-wide analysis of the SPL family transcription factors and their responses to abiotic stresses in maize

• A total of 31 SPL genes were identified in maize.
• The gene structure, motif compositions, phylogeny and chromosome locations were analyzed.
• The expansion of the ZmSPL genes mainly occurred due to segmental duplication.
• 19 ZmSPL genes were targets of microRNA miR156.
• Gene expression analysis suggests functional divergence of ZmSPL genes in maize.

SQUAMOSA promoter binding protein-like (SPL) transcription factors (TFs) are plant-specific and play vital regulatory roles in plant growth and development. Even though they are one of the unique groups of TFs in plants, their characteristics, evolutionary relationships and expression patterns are largely unknown in maize, an important food crop worldwide. In this study, we identified 31 SPL genes (ZmSPLs) in the maize B73 genome. A phylogenetic analysis showed that these genes were divided into six groups (Groups 1–6) and members within the same group shared conserved exon/intron distributions and motif compositions, implying their functional redundancy. The 31 ZmSPL genes were distributed unevenly on 9 of the 10 chromosomes, with 10 segmental duplication events, suggesting that the expansion of the ZmSPL genes occurred due to segmental duplication. Analysis of the Ka/Ks ratios showed that the duplicated ZmSPL genes had primarily undergone strong purifying selection. In addition, 19 of the 31 ZmSPLs, belonging to Groups 1, 2 and 3, were targets of microRNA miR156, indicating of the miR156-mediated posttranscriptional regulation of these ZmSPL genes. Expression analysis of the ZmSPLs in various tissues at different development stages revealed distinct spatiotemporal patterns. Moreover, quantitative real-time PCR analysis identified several ZmSPL genes that were potentially involved in response to abiotic stresses. Our results present a comprehensive overview of the maize SPL gene family and provide an important foundation for further uncovering the biological functions of ZmSPLs in the growth and development of maize.