Transcriptome analysis and association mapping reveal the genetic regulatory network response to cadmium stress in Populus tomentosa

Mingyang Quan; Xin Liu; Liang Xiao; Panfei Chen; Fangyuan Song; Wenjie Lu; Yuepeng Song; Deqiang Zhang

doi:10.1093/jxb/eraa434

Transcriptome analysis and association mapping reveal the genetic regulatory network response to cadmium stress in Populus tomentosa

J Exp Bot. 2021 Feb 2;72(2):576-591. doi: 10.1093/jxb/eraa434.

Authors

Mingyang Quan^{1

2

3}, Xin Liu^{2

3}, Liang Xiao^{2

3}, Panfei Chen^{2

3}, Fangyuan Song^{2

3}, Wenjie Lu^{2

3}, Yuepeng Song^{1

2

3}, Deqiang Zhang^{1

2

3}

Affiliations

¹ Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China.
² National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.
³ Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.

PMID: 32937662
DOI: 10.1093/jxb/eraa434

Abstract

Long non-coding RNAs (lncRNAs) play essential roles in plant abiotic stress responses, but the response of lncRNA-mediated genetic networks to cadmium (Cd) treatment remain elusive in trees, the promising candidates for phytoremediation of Cd contamination. We identified 172 Cd-responsive lncRNAs and 295 differentially expressed target genes in the leaves of Cd-treated Populus tomentosa. Functional annotation revealed that these lncRNAs were involved in various processes, including photosynthesis, hormone regulation, and phenylalanine metabolism. Association studies identified 78 significant associations, representing 14 Cd-responsive lncRNAs and 28 target genes for photosynthetic and leaf physiological traits. Epistasis uncovered 83 pairwise interactions among these traits, revealing Cd-responsive lncRNA-mediated genetic networks for photosynthesis and leaf physiology in P. tomentosa. We focused on the roles of two Cd-responsive lncRNA-gene pairs, MSTRG.22608.1-PtoMYB73 and MSTRG.5634.1-PtoMYB27, in Cd tolerance of Populus, and detected insertions/deletions within lncRNAs as polymorphisms driving target gene expression. Genotype analysis of lncRNAs and heterologous overexpression of PtoMYB73 and PtoMYB27 in Arabidopsis indicated their effects on enhancing Cd tolerance, photosynthetic rate, and leaf growth, and the potential interaction mechanisms of PtoMYB73 with abiotic stresses. Our study identifies the genetic basis for the response of Populus to Cd treatment, facilitating genetic improvement of Cd tolerance in trees.

Keywords: Populus; Association mapping; cadmium; epistasis; genetic architecture; leaf physiology; long non-coding RNAs; photosynthesis.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Cadmium / toxicity
Gene Expression Profiling
Gene Expression Regulation, Plant
Gene Regulatory Networks
Populus* / genetics

Substances

Cadmium