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Genomic organization, differential expression, and functional analysis of the SPL gene family in Gossypium hirsutum


SQUAMOSA promoter binding protein-like (SPL) genes encode plant-specific transcription factors that are involved in many fundamental developmental processes. Certain SPL genes contain sequences complementary to miR156, a microRNA (miRNA) that plays a role in modulating plant gene expression. In this study, 30 SPL genes were identified in the reference genome of Gossypium raimondii and 24 GhSPLs were cloned from Gossypium hirsutum. G. raimondii is regarded as the putative contributor of the D-subgenome of G. hirsutum. Comparative analysis demonstrated sequence conservation between GhSPLs and other plant species. GhSPL genes could be classified into seven subclades based on phylogenetic analysis, diverse intron–exon structure, and motif prediction. Within each subclade, genes shared a similar structure. Sequence and experimental analysis predicted that 18 GhSPL genes are putative targets of GhmiR156. Additionally, tissue-specific expression analysis of GhSPL genes showed that their spatiotemporal expression patterns during development progressed differently, with most genes having high transcript levels in leaves, stems, and flowers. Finally, overexpression of GhSPL3 and GhSPL18 in Arabidopsis plants demonstrated that these two genes are involved in the development of leaves and second shoots and play an integral role in promoting flowering. The flowering integrator GhSOC1 may bind to the promoter of GhSPL3 but not GhSPL18 to regulate flowering. In conclusion, our analysis of GhSPL genes will provide some gene resources and a further understanding of GhSPL3 and GhSPL18 function in flowering promotion. Furthermore, the comparative genomics and functional analysis deepened our understanding of GhSPL genes during upland cotton vegetative and reproductive growth.

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This research was funded by the National High-tech Research and Development Projects of China (2013AA102601) and supported by the Earmarked Fund for China Agriculture Research System (CARS-18).

Conflict of interest

The authors declare that they have no conflict of interest.

Author information

Correspondence to Chengshe Wang or Shuxun Yu.

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Communicated by S. Hohmann.

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Zhang, X., Dou, L., Pang, C. et al. Genomic organization, differential expression, and functional analysis of the SPL gene family in Gossypium hirsutum . Mol Genet Genomics 290, 115–126 (2015). https://doi.org/10.1007/s00438-014-0901-x

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  • Gossypium hirsutum
  • SPL
  • GhmiR156
  • Phylogenetic tree
  • Expression analysis