A novel single nucleotide mutation of TFL1 alters the plant architecture of Gossypium arboreum through changing the pre-mRNA splicing

Abstract Key message A single nucleotide mutation from G to A at the 201st position changed the 5′ splice site and deleted 31 amino acids in the first exon of GaTFL1 . Abstract Growth habit is an important agronomic trait that plays a decisive role in the plant architecture and crop yield. Cotton ( Gossypium ) tends to indeterminate growth, which is unsuitable for the once-over mechanical harvest system. Here, we identified a determinate growth mutant ( dt1 ) in Gossypium arboreum by EMS mutagenesis, in which the main axis was terminated with the shoot apical meristem (SAM) converted into flowers. The map-based cloning of the dt1 locus showed a single nucleotide mutation from G to A at the 201st positions in TERMINAL FLOWER 1 ( GaTFL1 ), which changed the alternative RNA 5′ splice site and resulted in 31 amino acids deletion and loss of function of GaTFL1 . Comparative transcriptomic RNA-Seq analysis identified many transporters responsible for the phytohormones, auxin, sugar, and flavonoids, which may function downstream of GaTFL1 to involve the plant architecture regulation. These findings indicate a novel alternative splicing mechanism involved in the post-transcriptional modification and TFL1 may function upstream of the auxin and sugar pathways through mediating their transport to determine the SAM fate and coordinate the vegetative and reproductive development from the SAM of the plant, which provides clues for the TFL1 mechanism in plant development regulation and provide research strategies for plant architecture improvement.