# Genome-Wide Analysis of the TIFY Gene Family in Litchi (Litchi chinensis Sonn.): Identification and Expression Profiling

## TL;DR

This study identifies 14 TIFY genes in litchi and finds that three of them are linked to fruit coloration, offering insights for improving litchi appearance through breeding.

## Contribution

The study is the first to characterize the TIFY gene family in litchi and identify specific genes involved in fruit color regulation.

## Key findings

- 14 TIFY genes were identified in litchi and classified into four subfamilies.
- LcPPD1, LcJAZ5, and LcJAZ7 are correlated with red pigment accumulation in litchi pericarp.
- Segmental duplication is a key driver for the expansion of LcTIFY genes.

## Abstract

Litchi is valued for its sweet taste and appealing red skin, but varieties like ‘Feizixiao’ often fail to turn fully red at harvest, reducing their commercial value. While the TIFY gene family is known to influence fruit coloring in other plants, its role in litchi was unknown. Herein, 14 TIFY genes were identified in the litchi, and their structures, evolution, and expression patterns were further characterized. Tissue-specific expression was observed among the LcTIFY genes. Notably, three genes—LcPPD1, LcJAZ5, and LcJAZ7—exhibited significant correlations with red pigment accumulation in the pericarp, with their expression levels responding to ABA (coloration promoter) and CPPU (coloration inhibitor) treatments during fruit coloring. These results offer new insights into the genetic control of litchi fruit color and provide valuable targets for breeding programs seeking to enhance fruit appearance and marketability.

The TIFY family, known as a novel group of transcription factors unique to the plant, plays a number of roles and has been functionally characterized in numerous plant species. However, TIFY proteins remain unexplored in litchi. Here, we identified 14 TIFY genes in litchi, which were unevenly located on 8 of 15 chromosomes. All of the LcTIFY proteins were predicted to be nuclear-localized and were phylogenetically categorized into four subfamilies (TIFY, PPD, ZML, and JAZ). Duplication analysis detected no tandem duplications but identified one segmental duplication event with LcTIFY genes, suggesting that segmental duplication served as the primary driving force for the expansion of LcTIFY genes. Comparative collinear analysis revealed 12, 5, and 27 collinear gene pairs between litchi and Arabidopsis, rice, and apple, respectively, providing valuable clues for understanding the evolution of the LcTIFY genes. RNA-Seq and qRT-PCR analyses indicated tissue-preferential expression patterns among LcTIFY genes. Notably, LcPPD1 and LcJAZ5 expressions were negatively correlated with anthocyanin accumulation in the ‘Feizixiao’ variety, except that LcJAZ5 displayed a positive correlation under CPPU treatment. In contrast, LcJAZ7 expression showed a positive correlation across all treatments, implicating these genes in the regulation of pericarp pigmentation. Collectively, these findings lay the groundwork for future investigations into the functional roles of TIFY genes in litchi and offer valuable genetic resources for elucidating the mechanisms underlying litchi pigmentation, thereby providing fresh perspectives for subsequent research into the molecular mechanisms of color formation in plants.