Comparative transcriptome analysis of cold-tolerant and -sensitive asparagus bean under chilling stress and recovery

Mingjun Miao; Huaqiang Tan; Le Liang; Haitao Huang; Wei Chang; Jianwei Zhang; Ju Li; Yi Tang; Zhi Li; Yunsong Lai; Liang Yang; Huanxiu Li

doi:10.7717/peerj.13167

Comparative transcriptome analysis of cold-tolerant and -sensitive asparagus bean under chilling stress and recovery

PeerJ. 2022 Mar 22:10:e13167. doi: 10.7717/peerj.13167. eCollection 2022.

Authors

Mingjun Miao^#^{1

2}, Huaqiang Tan^#³, Le Liang¹, Haitao Huang⁴, Wei Chang², Jianwei Zhang¹, Ju Li², Yi Tang¹, Zhi Li², Yunsong Lai¹, Liang Yang², Huanxiu Li¹

Affiliations

¹ College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China.
² Horticulture Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, China.
³ Chengdu Academy of Agriculture and Forestry Sciences, Chengdu, Sichuan, China.
⁴ Mianyang Academy of Agricultural Sciences, Mianyang, Sichuan, China.

^# Contributed equally.

Abstract

Background: Low temperature is a type of abiotic stress that threatens the growth and yield of asparagus bean. However, the key genes and regulatory pathways involved in low temperature response in this legume are still poorly understood. Methodology. The present study analyzed the transcriptome of seedlings from two asparagus bean cultivars-Dubai bean and Ningjiang 3-using Illumina RNA sequencing (RNA-seq). Correlations between samples were determined by calculating Pearson correlation coefficients (PCC) and principal component analysis (PCA). Differentially expressed genes (DEGs) between two samples were identified using the DESeq package. Transcription factors (TF) prediction, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of DEGs were also performed.

Results: Phenotypes and physiological indices indicated that Ningjiang 3 seedlings tolerated cold better than Dubai bean seedlings, in contrast to adult stage. The transcriptome dynamics of the two cultivars were closely compared using Illumina RNA-seq following 0, 3, 12, and 24 h of cold stress at 5 °C and recovery for 3 h at 25 °C room temperature. Global gene expression patterns displayed relatively high correlation between the two cultivars (>0.88), decreasing to 0.79 and 0.81, respectively, at 12 and 24 h of recovery, consistent with the results of principal component analysis. The major transcription factor families identified from differentially expressed genes between the two cultivars included bHLH, NAC, C2H2, MYB, WRKY, and AP2/ERF. The representative GO enrichment terms were protein phosphorylation, photosynthesis, oxidation-reduction process, and cellular glucan metabolic process. Moreover, KEGG analysis of DEGs within each cultivar revealed 36 transcription factors enriched in Dubai bean and Ningjiang 3 seedlings under cold stress.

Conclusions: These results reveal new information that will improve our understanding of the molecular mechanisms underlying the cold stress response of asparagus bean and provide genetic resources for breeding cold-tolerant asparagus bean cultivars.

Keywords: Asparagus bean; Cold stress; RNA-seq; Recovery; Sesquipedialis; Transcriptome.

Publication types

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

MeSH terms

Cold-Shock Response / genetics
Fabaceae* / genetics
Gene Expression Profiling
Plant Breeding
Seedlings / genetics
Transcription Factors / genetics
Transcriptome* / genetics

Substances

Transcription Factors

Grants and funding

This work was supported by the Experts of Sichuan Vegetable Innovation Team-Breeding of New Vegetable Varieties of Sichuan province (No. sccxtd-05, 2019-2023). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.