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Acta Agronomica Sinica ›› 2025, Vol. 51 ›› Issue (8): 2100-2110.doi: 10.3724/SP.J.1006.2025.55007

• CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS • Previous Articles     Next Articles

Identification and expression pattern analysis of the BnaDUF579 gene family in Brassica napus

WANG Bin**(), MENG Jiang-Yu**(), QIU Hao-Liang, HE Ya-Jun*(), QIAN Wei   

  1. College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
  • Received:2025-01-15 Accepted:2025-04-27 Online:2025-08-12 Published:2025-05-26
  • Contact: *E-mail: hyj790124@163.com
  • About author:

    **Contributed equally to this work

  • Supported by:
    National Natural Science Foundation of China(32272060);National Key Research and Development Program of China(2022YFD1200400);Natural Science Foundation of Chongqing(cstc2021jcyj-msxmx1198);Natural Science Foundation of Chongqing(CSTB2024NSCQ-MSX0423)

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Abstract:

The domain of unknown function 579 (DUF579) family is widely distributed across eukaryotes and plays a critical role in secondary cell wall development and xylan biosynthesis. However, a comprehensive investigation of BnaDUF579 genes in Brassica napus has not yet been reported. In this study, we performed a genome-wide identification and bioinformatic analysis of BnaDUF579 family members. Phylogenetic relationships, gene structure, conserved motif composition, chromosomal distribution, and collinearity were systematically analyzed. Additionally, tissue-specific expression patterns and promoter cis-acting elements were examined. A total of 31 BnaDUF579 genes were identified, of which 24 contained only a single exon. Based on sequence alignment and phylogenetic analysis, these genes were classified into four clades, Group1, Group2, Group3, and Group4. Genes within the same clade exhibited similar motif compositions, whereas those in different clades showed distinct differences. Evolutionary analysis revealed that the BnaDUF579 gene family is more closely related to that of B. oleracea than to B. rapa. Expression profiling showed that BnaDUF579 genes are predominantly expressed in the stem, root, silique, and seed tissues of rapeseed. Promoter analysis indicated that cis-acting elements associated with hormone responses, abiotic stress, tissue development, and light responsiveness are widely present. Overall, these findings enhance our understanding of the BnaDUF579 gene family and provide a foundation for future functional studies in Brassica napus.

Key words: Brassica napus, BnaDUF579, gene family, expression analysis, xyloglucan

Table 1

qRT-PCR primers used in this study"

基因名称
Gene name		 正向引物序列
Forward primer sequence (5′-3′)		 反向引物序列
Reverse primer sequence (5′-3′)
BnaActin7 GGAGCTGAGAGATTCCGTTG GAACCACCACTGAGGACGAT
BnaA09G0469400ZS CCTTCCCCAACCACCACT CGAAGACGAGGAGGTTGC
BnaA07G0280400ZS ACTTTCGCGGAGGAGTTCTT CCTGTAATCTCCACCGTCG
BnaC06G0382400ZS CGGCGGCTAGAGATAGAGAA GCTTCTTCGTGAAACCCAGTA
BnaC07G0206400ZS CTTCACCATCGCTTTTCTCCT CGTTGGCAACTGAGAGGTG
BnaA09G0107100ZS CGTCGACGAGAATCCTTACTTA GTTAGGTAAATCGTTGATCGCC

Table 2

Basic information of BnaDUF579 family members in Brassica napus"

数目
Number		 分支
Group		 基因名称
Gene ID		 蛋白长度
Protein length (aa)		 分子量
Molecular weight (Da)		 等电点
Isoelectric point
1 Group1 BnaC06G0104800ZS 296 33,691.33 8.03
2 Group1 BnaA09G0381200ZS 296 33,692.32 7.59
3 Group1 BnaA08G0293400ZS 281 31,840.50 7.57
4 Group1 BnaA05G0318700ZS 297 33,747.22 6.51
5 Group1 BnaC08G0195300ZS 281 31,835.56 8.35
6 Group1 BnaC06G0382400ZS 296 33,018.62 5.94
7 Group1 BnaA07G0326600ZS 296 33,077.72 6.31
8 Group1 BnaC02G0257800ZS 106 12,216.96 5.60
9 Group1 BnaC02G0257900ZS 163 17,749.29 5.13
10 Group2 BnaA03G0394800ZS 327 35,772.35 6.00
11 Group2 BnaA09G0469400ZS 324 36,052.89 6.60
12 Group2 BnaC08G0304500ZS 324 36,080.95 6.60
13 Group2 BnaC07G0206400ZS 315 35,596.34 7.18
14 Group2 BnaA07G0142200ZS 315 35,637.43 7.16
15 Group2 BnaC09G0093600ZS 308 34,733.51 6.82
16 Group2 BnaC03G0489400ZS 330 36,106.81 6.37
17 Group2 BnaA09G0107100ZS 323 35,524.20 7.12
18 Group2 BnaC09G0108200ZS 320 35,198.92 6.75
19 Group3 BnaC03G0580500ZS 139 15,392.55 8.93
20 Group3 BnaA07G0097300ZS 289 32,282.19 8.53
21 Group3 BnaC07G0148300ZS 289 32,328.22 8.52
22 Group3 BnaC06G0321200ZS 291 32,547.31 6.45
23 Group3 BnaA07G0280400ZS 291 32,535.25 6.24
24 Group3 BnaA09G0427700ZS 289 32,399.37 9.16
25 Group3 BnaC05G0239000ZS 289 32,399.37 9.16
26 Group3 BnaA02G0165700ZS 288 32,293.04 8.17
27 Group3 BnaC02G0212300ZS 295 33,182.18 8.67
28 Group4 BnaC07G0460400ZS 312 34,769.71 9.63
29 Group4 BnaC01G0183700ZS 311 34,904.00 9.57
30 Group4 BnaA01G0144700ZS 309 34,794.00 9.70
31 Group4 BnaA03G0482400ZS 312 34,980.20 9.74

Fig. 1

Phylogenetic analysis of DUF579 proteins in B. napus, A. thaliana, B. rapa and B. oleracea"

Fig. 2

Conserved motifs, conserved structural domains, and gene structure of the BnaDUF579 gene family in Brassica napus A: phylogenetic tree of BnaDUF579 proteins; B: conserved motifs of BnaDUF579 proteins; C: conserved structural domains of BnaDUF579; D: gene structure of BnaDUF579."

Fig. 3

Distribution of BnaDUF579s on chromosomes"

Fig. 4

Collinearity of DUF579s in A. thaliana, B. rapa, B. oleracea, and B. napus The red lines indicate orthologous DUF579 genes between B. napus and A. thaliana or B. oleracea. The two black lines indicate two orthologous DUF579 genes between B. napus and B. rapa."

Fig. 5

Expression levels of BnaDUF579 in different tissues and organs of B. napus A: expression pattern of BnaDUF579 in transcriptome data. B: expression levels of selected BnaDUF579 were verified by qRT-PCR."

Fig. 6

Cis-element analysis on the promoter regions of BnaDUF579 genes"

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