Identification and expression analysis of the bHLH gene family in Nitraria sibirica

ZHANG Jianjun, WU Jingxiang, FANG Hao, ZHU Liming, CHENG Tielong

Journal of Nanjing Forestry University (Natural Sciences Edition） ›› 2025, Vol. 49 ›› Issue (6) : 102-114.

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南京林业大学学报（自然科学版）
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Journal of Nanjing Forestry University (Natural Sciences Edition） ›› 2025, Vol. 49 ›› Issue (6) : 102-114. DOI: 10.12302/j.issn.1000-2006.202311.202404036

Identification and expression analysis of the bHLH gene family in Nitraria sibirica

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Abstract

【Objective】The basic helix-loop-helix (bHLH) transcription factors play critical roles in plant growth, metabolism, and responses to biotic/abiotic stresses. Genome-wide identification and bioinformatics analysis of the bHLH gene family in Nitraria sibirica will provide foundational insights for subsequent bHLH gene cloning and further biological studies.【Method】Bioinformatics and molecular biology approaches were employed to systematically analyze the phylogenetic relationships of the N. sibirica bHLH gene family at the genome-wide level. Transcriptome datasets and quantitative reverse transcription-PCR (qRT-PCR) were employed to analyze the response of the bHLH genes under to stress.【Result】A total of 88 bHLH transcription factors were identified from the N. sibirica genome, unevenly distributed across 12 chromosomes with two pairs of tandemly duplicated gene. Phylogenetic analysis classified these members into 16 distinct subclades. Cis-acting element analysis revealed that the 88 bHLH genes harbored multiple environment- and stress-responsive regulatory elements. Expression profiling demonstrated differential responses of N. sibirica bHLH genes to salt stress. qRT-PCR results further demonstrated that six bHLH genes (bHLH1, bHLH2, bHLH24, bHLH30, bHLH70 and bHLH73) exhibited pronounced tissue-specific expression patterns. Under salt stress, bHLH1, bHLH24, bHLH70 and bHLH73 were significantly upregulated in leaves, while bHLH2 and bHLH30 were down regulated in leaves. In roots, all six genes displayed marked upregulation. In stems, five genes (bHLH1, bHLH24, bHLH30, bHLH70 and bHLH73) were upregulated, whereas bHLH2 showed down regulation.【Conclusion】This study identified 88 conserved bHLH transcription factors in N. sibirica, characterized by conserved gene structures and protein domains, along with two tandem duplication events on chromosomes. The differential expression of bHLH genes in roots, stems and leaves under salt stress suggests their potential involvement in salt tolerance mechanisms. These findings establish a critical foundation for elucidating the functional roles of the bHLH transcription factor family in N. sibirica.

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Nitraria sibirica / bHLH transcription factors / salt stress / gene expression

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ZHANG Jianjun , WU Jingxiang , FANG Hao , et al . Identification and expression analysis of the bHLH gene family in Nitraria sibirica[J]. Journal of Nanjing Forestry University (Natural Sciences Edition）. 2025, 49(6): 102-114 https://doi.org/10.12302/j.issn.1000-2006.202311.202404036

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