Transcriptomic and Metabolomic Analysis Reveal the Cold Tolerance Mechanism of Common Beans Under Cold Stress

Overview

Journal BMC Plant Biol

Publisher Biomed Central

Specialty Biology

Date 2025 Mar 16

PMID 40089684

Authors

Wen Tang

Zixuan Li

Zeping Xu

Xiyu Sui

Le Liang

Jiachang Xiao

Xueping Song

Bo Sun

Zhi Huang

Yunsong Lai

Changquan Wang

Yi Tang

Huanxiu Li

Affiliations

Soon will be listed here.

Abstract

Background: Common bean (Phaseolus vulgaris L.) is a thermophilic crop, and exposure to cold stress can significantly impact their yield and quality. To elucidate the impact of cold stress on cold-tolerant 'Wei Yuan' (WY) and cold-sensitive 'Bai Bu Lao' (BBL) of common bean, the mechanism of cold tolerance was studied by physiological and biochemical and multi-omics analysis.

Results: In this study, lower relative conductivity and higher malondialdehyde content after cold stress endowed 'WY' seedlings with cold tolerance. A total of 11,837 differentially expressed genes (DEGs) and 923 differential metabolites (DEMs) were identified by transcriptome and metabolomics analysis. Joint analysis showed that under cold stress, DEGs and DEMs in common beans are extensively engaged in sugar, amino acid and isoflavonoid biosynthesis, flavone and flavonol biosynthesis, and plant hormone signal translation, especially related to isoflavone biosynthesis. In addition, it was also found that bHLH and MYB family transcription factors may be involved in the cold signal transduction of common bean.

Conclusions: The above results will provide a theoretical basis for the cold tolerance mechanism of common beans and provide help for the screening of cold-tolerant resources of common beans.

Clinical Trial Number: Not applicable.

References

Ding Y, Yang S . Surviving and thriving: How plants perceive and respond to temperature stress. Dev Cell. 2022; 57(8):947-958. DOI: 10.1016/j.devcel.2022.03.010. View

Nawaz M, Sun J, Shabbir S, Khattak W, Ren G, Nie X . A review of plants strategies to resist biotic and abiotic environmental stressors. Sci Total Environ. 2023; 900:165832. DOI: 10.1016/j.scitotenv.2023.165832. View

Bhat K, Mahajan R, Pakhtoon M, Urwat U, Bashir Z, Shah A . Low Temperature Stress Tolerance: An Insight Into the Omics Approaches for Legume Crops. Front Plant Sci. 2022; 13:888710. PMC: 9204169. DOI: 10.3389/fpls.2022.888710. View

Jha U, Bohra A, Jha R . Breeding approaches and genomics technologies to increase crop yield under low-temperature stress. Plant Cell Rep. 2016; 36(1):1-35. DOI: 10.1007/s00299-016-2073-0. View

Jan N, Rather A, John R, Chaturvedi P, Ghatak A, Weckwerth W . Proteomics for abiotic stresses in legumes: present status and future directions. Crit Rev Biotechnol. 2022; 43(2):171-190. DOI: 10.1080/07388551.2021.2025033. View

Waadt R, Seller C, Hsu P, Takahashi Y, Munemasa S, Schroeder J . Plant hormone regulation of abiotic stress responses. Nat Rev Mol Cell Biol. 2022; 23(10):680-694. PMC: 9592120. DOI: 10.1038/s41580-022-00479-6. View

Hong J, Yang L, Zhang D, Shi J . Plant Metabolomics: An Indispensable System Biology Tool for Plant Science. Int J Mol Sci. 2016; 17(6). PMC: 4926328. DOI: 10.3390/ijms17060767. View

Li Y, Tian Q, Wang Z, Li J, Liu S, Chang R . Integrated analysis of transcriptomics and metabolomics of peach under cold stress. Front Plant Sci. 2023; 14:1153902. PMC: 10083366. DOI: 10.3389/fpls.2023.1153902. View

Zhu X, Liao J, Xia X, Xiong F, Li Y, Shen J . Physiological and iTRAQ-based proteomic analyses reveal the function of exogenous γ-aminobutyric acid (GABA) in improving tea plant (Camellia sinensis L.) tolerance at cold temperature. BMC Plant Biol. 2019; 19(1):43. PMC: 6354415. DOI: 10.1186/s12870-019-1646-9. View

10.

Mu J, Fu Y, Liu B, Zhang Y, Wang A, Li Y . SiFBA5, a cold-responsive factor from Saussurea involucrata promotes cold resilience and biomass increase in transgenic tomato plants under cold stress. BMC Plant Biol. 2021; 21(1):75. PMC: 7863501. DOI: 10.1186/s12870-021-02851-8. View

11.

Isah T . Stress and defense responses in plant secondary metabolites production. Biol Res. 2019; 52(1):39. PMC: 6661828. DOI: 10.1186/s40659-019-0246-3. View

12.

Sun Q, Ma L, Zhu X . Metabolomics-based exploration the response mechanisms of Saussurea involucrata leaves under different levels of low temperature stress. BMC Genomics. 2023; 24(1):297. PMC: 10236807. DOI: 10.1186/s12864-023-09376-4. View

13.

Chen B, Wu X, Guo H, Xiao J . Effects of appropriate low-temperature treatment on the yield and quality of pigmented potato (Solanum tuberosum L.) tubers. BMC Plant Biol. 2024; 24(1):274. PMC: 11007950. DOI: 10.1186/s12870-024-04951-7. View

14.

Verma V, Ravindran P, Kumar P . Plant hormone-mediated regulation of stress responses. BMC Plant Biol. 2016; 16:86. PMC: 4831116. DOI: 10.1186/s12870-016-0771-y. View

15.

Khan T, Fariduddin Q, Yusuf M . Low-temperature stress: is phytohormones application a remedy?. Environ Sci Pollut Res Int. 2017; 24(27):21574-21590. DOI: 10.1007/s11356-017-9948-7. View

16.

Hu Y, Jiang Y, Han X, Wang H, Pan J, Yu D . Jasmonate regulates leaf senescence and tolerance to cold stress: crosstalk with other phytohormones. J Exp Bot. 2017; 68(6):1361-1369. DOI: 10.1093/jxb/erx004. View

17.

Gao X, Ma J, Tie J, Li Y, Hu L, Yu J . BR-Mediated Protein -Nitrosylation Alleviated Low-Temperature Stress in Mini Chinese Cabbage ( ssp. ). Int J Mol Sci. 2022; 23(18). PMC: 9503245. DOI: 10.3390/ijms231810964. View

18.

Gul N, Masoodi K, Ramazan S, Mir J, Aslam S . Study on the impact of exogenously applied methyl jasmonate concentrations on Solanum lycopersicum under low temperature stress. BMC Plant Biol. 2023; 23(1):437. PMC: 10508017. DOI: 10.1186/s12870-023-04449-8. View

19.

Zhang L, Jiang X, Liu Q, Ahammed G, Lin R, Wang L . The HY5 and MYB15 transcription factors positively regulate cold tolerance in tomato via the CBF pathway. Plant Cell Environ. 2020; 43(11):2712-2726. DOI: 10.1111/pce.13868. View

20.

Panahi B, Shahi A . Trancriptome data mining in combination with co-expression network analysis identifies the functional modules and critical regulators in L. in response to cold stress. Biochem Biophys Rep. 2023; 37:101620. PMC: 10753052. DOI: 10.1016/j.bbrep.2023.101620. View