Genome-wide identification and characterization of NHL gene family in response to alkaline stress, ABA and MEJA treatments in wild soybean (Glycine soja)

Xu Zhang; Yongguo Xue; Haihang Wang; Zaib Un Nisa; Xiaoxia Jin; Lijie Yu; Xinlei Liu; Yang Yu; Chao Chen

doi:10.7717/peerj.14451

Genome-wide identification and characterization of NHL gene family in response to alkaline stress, ABA and MEJA treatments in wild soybean (Glycine soja)

PeerJ. 2022 Dec 2:10:e14451. doi: 10.7717/peerj.14451. eCollection 2022.

Authors

Xu Zhang^#¹, Yongguo Xue^#², Haihang Wang¹, Zaib Un Nisa³, Xiaoxia Jin¹, Lijie Yu¹, Xinlei Liu², Yang Yu⁴, Chao Chen¹

Affiliations

¹ Harbin Normal University, Harbin, Heilongjiang, China.
² Heilongjiang Provincial Academy of Agricultural Sciences, Harbin, Heilongjiang, China.
³ University of Lahore, Lahore, Pakistan.
⁴ Shenyang University, Shenyang, China.

^# Contributed equally.

Abstract

Background: NDR1/HIN1-like (NHL) family genes are known to be involved in pathogen induced plant responses to biotic stress. Even though the NHL family genes have been identified and characterized in plant defense responses in some plants, the roles of these genes associated with the plant abiotic stress tolerance in wild soybean is not fully established yet, especially in response to alkaline stress.

Methods: We identified the potential NHL family genes by using the Hidden Markov model and wild soybean genome. The maximum-likelihood phylogenetic tree and conserved motifs were generated by using the MEME online server and MEGA 7.0 software, respectively. Furthermore, the syntenic analysis was generated with Circos-0.69. Then we used the PlantCARE online software to predict and analyze the regulatory cis-acting elements in promoter regions. Hierarchical clustering trees was generated using TM4: MeV4.9 software. Additionally, the expression levels of NHL family genes under alkaline stress, ABA and MEJA treatment were identified by qRT-PCR.

Results: In this study, we identified 59 potential NHL family genes in wild soybean. We identified that wild soybean NHL family genes could be mainly classified into five groups as well as exist with conserved motifs. Syntenic analysis of NHL family genes revealed genes location on 18 chromosomes and presence of 65 pairs of duplication genes. Moreover, NHL family genes consisted of a variety of putative hormone-related and abiotic stress responsive elements, where numbers of methyl jasmonate (MeJA) and abscisic acid (ABA) responsive elements were significantly larger than other elements. We confirmed the regulatory roles of NHL family genes in response to alkaline stress, ABA and MEJA treatment. In conclusion, we identified and provided valuable information on the wild soybean NHL family genes, and established a foundation to further explore the potential roles of NHL family genes in crosstalk with MeJA or ABA signal transduction mechanisms under alkaline stress.

Keywords: ABA; Alkaline stress; MeJA; NHL family genes; Wild soybean.

Publication types

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

MeSH terms

Abscisic Acid* / metabolism
Fabaceae* / genetics
Glycine / genetics
Glycine max / genetics
Phylogeny

Substances

Abscisic Acid
Glycine

Grants and funding

This work was supported by the Natural and Science Foundation of China (grant number 32001454), the Natural Science Foundation of Heilongjiang Province (grant number LH2020C068), the China Postdoctoral Science Foundation (2022M711431), the Scientific Research Project of Innovative Talents in Heilongjiang Province (grant number UNPYSCT-2020125) and the Joint guidance project of Department of Science and Technology of Heilongjiang Province (LH2021C052). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.