Guodong Zhang1,2,3,4, Xin Jin3,5, Xiubao Li6, Ning Zhang3,5, Shaoqian Li7, Huaijun Si8,9, Om P Rajora10, Xiu-Qing Li11. 1. College of Agronomy, Gansu Agricultural University, Lanzhou, China. 2. Department of Biology, Xinzhou Teachers University, Xinzhou, Shanxi, China. 3. Gansu Provincial Key Laboratory of Arid Land Crop Science, Gansu Key Laboratory of Crop Genetic and Germplasm Enhancement, Gansu Agricultural University, Lanzhou, China. 4. Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Fredericton, NB, E3B 4Z7, Canada. 5. College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China. 6. Rizhao Academy of Agricultural Sciences, Rizhao, China. 7. Qingdao Customs of the People's Republication of China, Shinan, Qingdao, 266001, China. 8. Gansu Provincial Key Laboratory of Arid Land Crop Science, Gansu Key Laboratory of Crop Genetic and Germplasm Enhancement, Gansu Agricultural University, Lanzhou, China. hjsi@gsau.edu.cn. 9. College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China. hjsi@gsau.edu.cn. 10. Faculty of Forestry and Environmental Management, University of New Brunswick, Fredericton, NB, E3B 5A3, Canada. Om.Rajora@unb.ca. 11. Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Fredericton, NB, E3B 4Z7, Canada. Xiu-Qing.Li@Canada.Ca.
Abstract
BACKGROUND: The phosphatidylethanolamine-binding protein (PEBP) gene family is involved in regulating many plant traits. Genome-wide identification of PEPB members and knowledge of their responses to heat stress may assist genetic improvement of potato (Solanum tuberosum). METHODS AND RESULTS: We identified PEBP gene family members from 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 their heat-induced gene expression using RT-PCR and RNA-Seq. Fifteen PEBP family genes were identified from DM v6.1 and named as StPEBP1 to StPEBP15 based on their locations on 6 chromosomes and were classified into FT, TFL, MFT, and PEBP-like subfamilies. Most of the StPEBP genes were found to have conserved motifs 1 to 5. Tandem or segmental duplications were found between StPEBP genes in seven pairs. Heat stress induced opposite expression patterns of certain FT and TFL members but involving different members in leaves, roots and tubers. CONCLUSION: The long-reads-based genome assembly and annotation provides a better genomic resource for identification of PEBP family genes. Heat stress tends to decrease FT gene activities but increases TFL gene activities, but this opposite expression involves different FT/TFL pairs in leaves, roots, and tubers. This tissue-specific expression pattern of PEBP members may partly explain why different potato organs differ in their sensitivities to heat stress. Our study provides candidate PEBP family genes and relevant information for genetic improvement of heat tolerance in potato and may help understand heat-induced responses in other plants.
BACKGROUND: The phosphatidylethanolamine-binding protein (PEBP) gene family is involved in regulating many plant traits. Genome-wide identification of PEPB members and knowledge of their responses to heat stress may assist genetic improvement of potato (Solanum tuberosum). METHODS AND RESULTS: We identified PEBP gene family members from 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 their heat-induced gene expression using RT-PCR and RNA-Seq. Fifteen PEBP family genes were identified from DM v6.1 and named as StPEBP1 to StPEBP15 based on their locations on 6 chromosomes and were classified into FT, TFL, MFT, and PEBP-like subfamilies. Most of the StPEBP genes were found to have conserved motifs 1 to 5. Tandem or segmental duplications were found between StPEBP genes in seven pairs. Heat stress induced opposite expression patterns of certain FT and TFL members but involving different members in leaves, roots and tubers. CONCLUSION: The long-reads-based genome assembly and annotation provides a better genomic resource for identification of PEBP family genes. Heat stress tends to decrease FT gene activities but increases TFL gene activities, but this opposite expression involves different FT/TFL pairs in leaves, roots, and tubers. This tissue-specific expression pattern of PEBP members may partly explain why different potato organs differ in their sensitivities to heat stress. Our study provides candidate PEBP family genes and relevant information for genetic improvement of heat tolerance in potato and may help understand heat-induced responses in other plants.
Keywords:
Abiotic stress response; Expression patterns; High temperature stress; PEBP gene family analysis; PEBP motifs; Phylogenetic relationships; Solanum tuberosum L.; Tandem and segmental duplications
Authors: Cristina Navarro; José A Abelenda; Eduard Cruz-Oró; Carlos A Cuéllar; Shojiro Tamaki; Javier Silva; Ko Shimamoto; Salomé Prat Journal: Nature Date: 2011-09-25 Impact factor: 49.962