Innovation and Emerging Roles of TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR Transcription Factors in Abiotic Stresses by Whole-Genome Duplication.

The TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR (TCP) family proteins are plant-specific transcription factors that have been well-acknowledged for designing the architectures of plant branch, shoot, and inflorescence. However, evidence for their innovation and emerging role in abiotic stress has been lacking. In this study, we identified a total of 36 genes in , 50% more than that in (i.e., 24). Comparative intra-genomes showed that such significant innovation was mainly due to the most recent whole genome duplication (rWGD) in lineage around Cretaceous-Paleogene (K-Pg) boundary after the divergence from . Transcriptome analysis showed that the expressions of genes varied among leaf, stem, and root, and they could also be elaborately regulated by abiotic stresses (e.g., cold and salt). Moreover, co-expression network identified a cold-associated regulatory module including , , and . Of them, was rWGD-duplicated from and evolved a strong capability of cold induction, which might suggest a neofunctionalization of genes and contribute to the adaptation of lineage during the Cenozoic global cooling. Evidentially, overexpression of into increased freezing tolerance and salt susceptibility. Integrating co-expression network and regulatory element analysis confirmed that PtrTCP10 can regulate the well-known cold- and salt-relevant genes (e.g., , , and ), proving that PtrTCP10 is an evolutionary innovation in response to environmental changes. Altogether, our results provide evidence of the rWGD in responsible for the innovation of genes and their emerging roles in environmental stresses.