Phenylalanine ammonia-lyase family is closely associated with response to phosphate deficiency in rice

  • Yun-Shil Gho
  • Sang-jin Kim
  • Ki-Hong JungEmail author
Research Article



Phenylalanine ammonia-lyase (PAL) catalyzes the first step in the biosynthetic phenylpropanoid pathway (PPP) via deamination of phenylalanine to trans-cinnamic acid, a precursor for the lignin and flavonoid biosynthetic pathways. Although its role is well-established in various plants, the functional significance of PAL genes in rice remains poorly understood.


This study aims to find out the global feature of rice PAL genes associated with phosphate use efficiency.


To identify the biological functions of individual rice PAL genes, we performed meta-expression profiling analysis based on phylogenomics of rice PAL genes and confirmed the expression patterns using Quantitative real-time PCR (qPCR).


We identified nine genes that were remarkably up-regulated during long-term phosphate (Pi) starvation and recovery processes through RNA-Seq data analysis. Expression patterns of the nine rice PAL genes under Pi starvation were further confirmed by qPCR, indicating that the function of PAL genes is strongly associated with Pi starvation response in rice.


Our study reports the functional significance of rice PAL genes involved in adaptation to low Pi growth conditions and provides useful information to improve Pi use efficiency in crop plant.


Phenylalanine ammonia-lyase Rice Phosphate starvation PAL gene family Transcriptome 





Anthocyanidin synthase


Chalcone isomerase


Chalcone synthase


Cis-acting regulatory element


Dihydroflavonol 4-reductase


Flavanone 3-hydroxylase


Fragments per kilobase of transcript per million mapped reads


Phenylalanine ammonia-lyase


Phenylpropanoid pathway




Salicylic acid


Quantitative real-time PCR



This work was supported by grants from the Next-Generation BioGreen 21 Program (grant number, PJ01325901 to KHJ) supported by the Rural Development Administration, and the National Research Foundation of Korea (NRF) (NRF-2016R1D1A1A09919568 to KHJ), Republic of Korea.

Supplementary material

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Supplementary material 1 (DOCX 18 kb)
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Supplementary material 2 (DOCX 20 kb)
13258_2019_879_MOESM3_ESM.eps (3.3 mb)
Supplementary material 3 (EPS 3419 kb)


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Copyright information

© The Genetics Society of Korea 2019

Authors and Affiliations

  1. 1.Graduate School of Biotechnology & Crop Biotechnology InstituteKyung Hee UniversityYonginSouth Korea

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