Genome-wide Identification of the DABB Gene Family in Brassica rapa ssp. pekinensis and Expression Analysis under Saline and Alkali Stress

doi:10.13560/j.cnki.biotech.bull.1985.2024-0817

Abstract

Abstract:

Objective DABB (dimeric α+β barrel domain protein) is a kind of protein containing 1‒2 dimerized α+β barrel domains, which plays roles in the responses of various plants to stress. This work aims to predict the properties of DABB proteins in Chinese cabbage (Brassica rapa ssp. pekinensis), investigate the expression changes of these genes in response to salt-alkali stress in Chinese cabbage varieties with different salt-alkali stress tolerances, and provide theoretical evidence for studying the resistant functions of DABB proteins in Chinese cabbage. Method The DABB gene family of Chinese cabbage was identified genome-widely by bioinformatics methods, and the genetic relationship, physical and chemical properties of the encoded proteins, chromosome localizations and gene structures were analyzed, real-time fluorescence quantitative PCR was used to analyze the expression patterns of these genes in different Chinese cabbage varieties under salt-alkali stress. Result A total of 7 DABB genes were identified in the genome of Chinese cabbage, distributed in 5 chromosomes, the DABBs with close relatives were similar in structure; the amino acid number of the encoded protein was 79-495 aa, the relative molecular weight was 8.94-54.19 kD, most of them were stable proteins, and subcellular localization prediction showed that most of the DABB proteins were located in the plasma membrane. Under salt-alkali stress treatments, 6 DABB genes of Chinese cabbage performed differentially expression response, but the expression patterns were different in the Chinese cabbage cultivars with different salt-alkali stress tolerance. Conclusion Totally 7 genes encoding the protein containing DABB domains are identified in the Chinese cabbage genome, 6 of them show differentially expression response under salt-alkali stress treatments, the different expression patterns of these genes may be related to the salt-alkali stress tolerance of Chinese cabbage.

Key words: Chinese cabbage, DABB gene, salt-alkali stress, genome-wide identification, expression analysis

SUN Tian-guo, YI Lan, QIN Xu-yang, QIAO Meng-xue, GU Xin-ying, HAN Yi, SHA Wei, ZHANG Mei-juan, MA Tian-yi. Genome-wide Identification of the DABB Gene Family in Brassica rapa ssp. pekinensis and Expression Analysis under Saline and Alkali Stress[J]. Biotechnology Bulletin, 2025, 41(4): 156-165.

Figures/Tables 9

Table 1 Primers information for RT-qPCR

引物名称 Primer name	引物序列 Primer sequence （5′-3′）
BrcActin-F	GGAGCTGAGAGATTCCGTTG
BrcActin-R	GAACCACCACTGAGGACGAT
BrcDABB1-1-F	CCGACGAGACCAAGAAGGAGATTATG
BrcDABB1-1-R	CTACGAAGGAGGAGGAACCAAGAAC
BrcDABB1-2-F	GGATGCTAAGTCGGAGATTGTGGATGTG
BrcDABB1-2-R	ACCCAGAAACCAAACCAGAAGGAACC
BrcDABB1-3-F	ATGGATGTGGTTAAGGAGAAGTCTGC
BrcDABB1-3-R	AAGGTACAACGAACTCAACAACAATGG
BrcDABB2-F	TCACGAGATGCTTAGACAAGGATTCAC
BrcDABB2-R	GAGAACTCAACGTGAAGAGGATGGCC
BrcDABB3-F	CTAAGGCTGATGAGATCTTGAAGGGCTC
BrcDABB3-R	GGCGACGGTGAAGTCAAGAATCACG
BrcHS1-1-F	GGAAGCAAAGGGACCAGTGAAGC
BrcHS1-1-R	AGTCTATGACCAGCACTTTATCCAAGC
BrcHS1-2-F	GGAAGCAAAGGGACCAGTGAAGC
BrcHS1-2-R	TGTAGTCTATAACCAACACTTTATCCAAGC

Fig. 1 Phylogenetic analysis of Chinese cabbage (Brassica rapa ssp. pekinensis) and Arabidopsis DABB proteins

Table 2 Membership information and property prediction of Chinese cabbage DABB protein family

蛋白质 Protein	基因座位号 Gene locus number	氨基酸数量 Number of amino acids/aa	相对分子质量 Relative molecular mass/kD	理论等电点 Theoretical isoelectric point	不稳定系数 Instability coefficient	平均疏水系数 Average hydrophobicity	亚细胞定位预测 Prediction of subcellular localizations
BrcDABB1-1	BraA08g002970.4C	201	22.328 56	5.27	30.79	-0.125	叶绿体 Chloroplast
BrcDABB1-2	BraA01g031610.4C	495	54.185 79	9.01	59.22	-0.159	细胞核 Nucleus
BrcDABB1-3	BraA05g019150.4C	187	20.350 27	4.87	37.96	-0.034	细胞质膜 Cell membrane
BrcDABB2	BraA10g019230.4C	111	12.321 08	5.22	22.95	0.109	细胞质膜 Cell membrane
BrcDABB3	BraA02g010040.4C	111	12.429 29	5.92	35.71	-0.009	细胞质膜 Cell membrane
BrcHS1-1	BraA01g037190.4C	107	12.111 95	5.41	27.24	-0.085	细胞质基质 Cytoplasm
BrcHS1-2	BraA01g037170.4C	79	8.936 29	5.21	19.30	-0.059	叶绿体 Chloroplast

Fig. 2 Analysis of conserved motifs (A) and structural domains (B) of Chinese cabbage DABB proteins

Fig. 3 Structure of Chinese cabbage DABB genes

Fig. 4 Distribution of cis-acting elements predicted in the promoters of Chinese cabbage DABB genesTC-rich repeats is a stress response element; TATC-box, GARE-motif, P-box are gibberellin response elements; LTR is a cold stress response element; TCA-element and SARE are salicylic acid response elements; ABRE is an abscisic acid response element; ARE is an antioxidant response element; AuxRR-core is a growth hormone response element; G-Box, GT1-motif are light response elements; RY-element is a cis-acting regulatory element involved in seed-specific regulation; CGTCA-motif, TGACG motif are methyl jasmonate response elements; CAT-box is an element related to the expression of meristematic tissue; GCN4-motif is a element involved in endosperm expression; MBS is a drought stress response element; CCAAT-box, MRE and MBSI are MYBHv1 binding sites, MYB binding sites are involved in light response and MYB binding sites are involved in gene regulation of flavonoid biosynthesis

Fig. 5 Expression analysis of Chinese cabbage DABB genes in different tissuesDifferent colors indicate relative expression

Fig. 6 Expression analysis of Chinese cabbage DABB genes under NaCl treatment of different concentrationsDifferent lowercase letters indicate significant differences (P<0.05); JT is ‘Jinxiaotong’ cultivar, and RC is ‘Ribenchunqiu’ cultivar. The same below

Fig. 7 Expression analysis of Chinese cabbage DABB genes under Na2CO3 treatment of different concentrations

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