Genome-Wide Identification of PEBP Gene Family Members In Potato and Their Phylogenetic Relationships and Expression Patterns Under Heat Stress

Abstract

The phosphatidy ethanolamine-binding protein (PEBP) genes are involved in regulating plant flowering and tuberization. We analyzed both the recently updated, long-reads-based reference genome (DM v6.1) and the previous short-reads-based annotation (PGSC DM v3.4) of the potato reference genome and characterized heat-induced gene expression using RT-PCR and RNA-Seq. Fifteen PEBP genes were identified from DM v6.1 and named StPEBP1 to StPEBP15 based on their chromosomal locations. Six of these genes were not found in the previous annnotation (DM v3.4). The 15 genes could be classified into FT, TFL, MFT, and PEBP-like subfamilies and were located on 6 chromosomes. Most of the StPEBP genes were found to have conserved motifs 1 to 5 similar to Arabidopsis and other plants. We found that heat stress induced opposite expression patterns of certain FT and TFL members in a tissue-specific way: StPEBP14 and StPEBP15 versus StPEBP3 and StPEBP10 in leaves, StPEBP4 versus StPEBP10 in roots, and StPEBP9 versus StPEBP3 in tubers (FT versus TFL respectively). This maintenance of the FT/TFL opposite expression pattern but involving tissue-specific PEBP members may partly explain why different potato organs have different sensitivities to heat stress. Our study provided important multiuse genomic resource, and relevant information and candidate genes for genetic improvement of heat tolerance in potato. It clearly support that the long-reads-based genome assembly and annotation provides a better genomic resource for identification of PEBP and perhaps other genes.

Physiological and Molecular Responses of Projected Future Temperatures on Potato Tuberization

“…During tuber initiation, StSP6A forms the tuberigen activation complex (TAC) in the stolon tips with FD-like proteins StFDL1a and StFDL1b, which are basic leucine zipper (bZIP) transcription factors (Teo et al, 2017). StSP6A is part of the PHOSPHATIDYLETHANOLAMINE BINDING PROTEINS (PEBP) family along with 14 other genes related to flowering/tuberization (Zhang et al, 2022). Under heat stress, it is known that during early stages of tuberization, StSP6A is inhibited post-transcriptionally through RNAbased interference by a small RNA called SUPPRESSING EXPRESSION OF SP6A (SES), while transcriptional regulation of StSP6A is the main regulation process in later stages of tuber development under heat stress (Lehretz et al, 2019;Park et al, 2022).…”