欢迎访问作物学报，今天是
作物学报

作物学报 ›› 2025, Vol. 51 ›› Issue (8): 2100-2110.doi: 10.3724/SP.J.1006.2025.55007

• 作物遗传育种·种质资源·分子遗传学 • 上一篇    下一篇

甘蓝型油菜BnaDUF579基因家族的鉴定与表达模式分析

王彬**(), 蒙姜宇**(), 邱浩良, 贺亚军*(), 钱伟   

  1. 西南大学农学与生物科技学院, 重庆 400716
  • 收稿日期:2025-01-15 接受日期:2025-04-27 出版日期:2025-08-12 网络出版日期:2025-05-26
  • 通讯作者: *贺亚军, E-mail: hyj790124@163.com
  • 作者简介:王彬, E-mail: 1666842119@qq.com;
    蒙姜宇, E-mail: 13002363008@163.com

    **同等贡献

  • 基金资助:
    国家自然科学基金项目(32272060);国家重点研发计划项目(2022YFD1200400);重庆市自然科学基金(cstc2021jcyj-msxmx1198);重庆市自然科学基金(CSTB2024NSCQ-MSX0423)

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 Published:2025-08-12 Published online: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)

RichHTML

1

PDF

48

摘要：

Domain of unknown function 579 (DUF579)家族广泛存在于真核生物中, 该家族在次生细胞壁发育和木聚糖生物合成中发挥着重要的作用。目前, 还没有研究系统报道过甘蓝型油菜BnaDUF579基因家族。本研究通过生物信息学方法对甘蓝型油菜BnaDUF579基因家族进行进化树构建、基因结构和保守基序分析、染色体分布和共线性分析、组织表达分析、启动子顺式作用元件分析。结果表明, 甘蓝型油菜BnaDUF579家族成员有31个, 其中的24个成员都只有1个外显子、没有内含子。这些基因分为4个分支, 包括Group1、Group2、Group3和Group4。同一分支内的成员具有相似的基序组成, 但不同分支之间的成员在基序组成上存在明显差异。该家族与白菜亲缘关系较远、与甘蓝亲缘关系更近。BnaDUF579基因家族主要在油菜茎、根、角果和种子中表达, 其启动子顺式作用元件涉及激素反应、对非生物胁迫的反应、组织发育、光响应等生理过程。以上研究结果丰富了对甘蓝型油菜BnaDUF579基因的认识, 为油菜BnaDUF579基因的功能研究奠定了基础。

关键词: 甘蓝型油菜, BnaDUF579, 基因家族, 表达分析, 木聚糖

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

表1

本研究中用到的qRT-PCR引物"

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

表2

甘蓝型油菜BnaDUF579家族成员基本信息表"

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

图1

甘蓝型油菜、拟南芥、白菜型油菜和甘蓝中DUF579蛋白的系统进化分析"

图2

甘蓝型油菜BnaDUF579基因家族的保守基序、保守结构域和基因结构 A: BnaDUF579蛋白的系统进化分析; B: 保守基序分析; C: BnaDUF579的保守结构域; D: BnaDUF579基因结构。"

图3

甘蓝型油菜BnaDUF579基因在染色体上的分布"

图4

甘蓝型油菜与拟南芥、白菜和甘蓝DUF579基因的共线性关系 红色线条表示甘蓝型油菜BnaDUF579基因与拟南芥、甘蓝的直系同源基因对应关系, 黑色线条表示甘蓝型油菜BnaDUF579基因与白菜的直系同源基因对应关系。"

图5

BnaDUF579基因在甘蓝型油菜不同组织和器官的表达模式 A: 转录组数据中BnaDUF579基因的表达模式。B: 通过qRT-PCR验证部分BnaDUF579基因的表达量。"

图6

BnaDUF579基因的启动子顺式作用元件分析"

[1] Mistry J, Chuguransky S, Williams L, Qureshi M, Salazar G A, Sonnhammer E L L, Tosatto S C E, Paladin L, Raj S, Richardson L J, et al. Pfam:the protein families database in 2021. Nucleic Acids Res, 2021, 49: D412-D419.
[2] Bateman A, Coggill P, Finn R D. DUFs: families in search of function. Acta Crystallogr Sect F Struct Biol Cryst Commun, 2010, 66: 1148-1152.
doi: 10.1107/S1744309110001685 pmid: 20944204
[3] Lyu P, Wan J, Zhang C, Hina A, Al Amin G M, Begum N, Zhao T. Unraveling the diverse roles of neglected genes containing domains of unknown function (DUFs): progress and perspective. Int J Mol Sci, 2023, 24: 4187.
[4] Luo C, Akhtar M, Min W, Bai X, Ma T, Liu C. Domain of unknown function (DUF) proteins in plants: function and perspective. Protoplasma, 2024, 261: 397-410.
[5] 张艺, 王晓晶, 赵淑清. 拟南芥DUF647家族成员RUS4植物表达载体的构建及亚细胞定位. 分子植物育种, 2020, 18: 444-449.
Zhang Y, Wang X J, Zhao S Q. Construction of the plant expression vector and subcellular localization of DUF647 family member RUS4 in Arabidopsis thaliana. Mol Plant Breed, 2020, 18: 444-449 (in Chinese with English abstract).
[6] 李文超, 张艺, 赵淑青. 拟南芥RUS4基因沉默对花药药室内壁次生加厚的影响. 中国细胞生物学学报, 2019, 41: 619-626.
Li W C, Zhang Y, Zhao S Q. Silencing of Arabidopsis RUS4 impairs anther endothecium secondary cell wall thickening. Chin J Cell Biol, 2019, 41: 619-626 (in Chinese with English abstract).
[7] 姜身飞, 谢云杰, 李乐乐, 王昱澎, 蔡秋华, 谢华安, 张建福. 水稻未知功能结构域基因OsDUF6的抗体制备. 福建农业学报, 2020, 35(2): 117-123.
Jiang S F, Xie Y J, Li L L, Wang Y P, Cai Q H, Xie H A, Zhang J F. Preparation of antibody for OsDUF6 with unknown functional domain from Oryzae sativa. Fujian J Agric Sci, 2020, 35(2): 117-123 (in Chinese with English abstract).
[8] Chen G, Cao X, Ma Z, Tang Y, Zeng Y, Chen L, Ye D, Zhang X. Overexpression of the nuclear protein gene AtDUF4 increases organ size in Arabidopsis thaliana and Brassica napus. J Genet Genomics, 2018, 45: 459-462.
[9] 戴丽诗, 常玮, 张赛, 钱明超, 黎小东, 张凯, 李加纳, 曲存民, 卢坤. Bna-novel-miR36421调节拟南芥株型和花器官发育的功能验证. 作物学报, 2022, 48: 1635-1644.
doi: 10.3724/SP.J.1006.2022.14106
Dai L S, Chang W, Zhang S, Qian M C, Li X D, Zhang K, Li J N, Qu C M, Lu K. Functional validation of Bna-novel-miR36421 regulating plant architecture and flower organ development in Arabidopsis thaliana. Acta Agron Sin, 2022, 48: 1635-1644 (in Chinese with English abstract).
doi: 10.3724/SP.J.1006.2022.14106
[10] Yuan Y, Teng Q, Zhong R, Ye Z H. TBL3 and TBL31, two Arabidopsis DUF231 domain proteins, are required for 3-O- monoacetylation of xylan. Plant Cell Physiol, 2016, 57: 35-45.
[11] Gao Y, Badejo A A, Sawa Y, Ishikawa T. Analysis of two L-Galactono-1,4-lactone-responsive genes with complementary expression during the development of Arabidopsis thaliana. Plant Cell Physiol, 2012, 53: 592-601.
[12] Yang S Q, Li W Q, Miao H, Gan P F, Qiao L, Chang Y L, Shi C H, Chen K M. REL2, a gene encoding an unknown function protein which contains DUF630 and DUF632 domains controls leaf rolling in rice. Rice, 2016, 9: 37.
[13] Yan D W, Zhou Y, Ye S H, Zeng L J, Zhang X M, He Z H. Beak-shaped grain 1/TRIANGULAR HULL 1, a DUF640 gene, is associated with grain shape, size and weight in rice. Sci China Life Sci, 2013, 56: 275-283.
[14] Cui Y, Wang M, Zhou H, Li M, Huang L, Yin X, Zhao G, Lin F, Xia X, Xu G. OsSGL a novel DUF1645 domain-containing protein, confers enhanced drought tolerance in transgenic rice and Arabidopsis. Front Plant Sci, 2016, 7: 2001.
[15] Kim J M, Woo D H, Kim S H, Lee S Y, Park H Y, Seok H Y, Chung W S, Moon Y H. Arabidopsis MKKK20 is involved in osmotic stress response via regulation of MPK6 activity. Plant Cell Rep, 2012, 31: 217-224.
[16] Luo C, Guo C, Wang W, Wang L, Chen L. Overexpression of a new stress-repressive gene OsDSR2 encoding a protein with a DUF966 domain increases salt and simulated drought stress sensitivities and reduces ABA sensitivity in rice. Plant Cell Rep, 2014, 33: 323-336.
[17] Song D, Sun J, Li L. Diverse roles of PtrDUF579 proteins in Populus and PtrDUF579-1 function in vascular cambium proliferation during secondary growth. Plant Mol Biol, 2014, 85: 601-612.
[18] Smith P J, O’Neill M A, Backe J, York W S, Peña M J, Urbanowicz B R. Analytical techniques for determining the role of domain of unknown function 579 proteins in the synthesis of O-methylated plant polysaccharides. SLAS Technol, 2020, 25: 345-355.
[19] Li M, Chen F, Luo J, Gao Y, Cai J, Zeng W, Doblin M S, Huang G, Xu W. The DUF579 proteins GhIRX15s regulate cotton fiber development by interacting with proteins involved in xylan synthesis. Crop J, 2024, 12: 1112-1125.
doi: 10.1016/j.cj.2024.07.006
[20] Lee C, Teng Q, Zhong R, Yuan Y, Haghighat M, Ye Z H. Three Arabidopsis DUF579 domain-containing GXM proteins are methyltransferases catalyzing 4-O-methylation of glucuronic acid on xylan. Plant Cell Physiol, 2012, 53: 1934-1949.
[21] Temple H, Mortimer J C, Tryfona T, Yu X, Lopez-Hernandez F, Sorieul M, Anders N, Dupree P. Two members of the DUF579 family are responsible for Arabinogalactan methylation in Arabidopsis. Plant Direct, 2019, 3: e00117.
[22] Li X, Jackson P, Rubtsov D V, Faria-Blanc N, Mortimer J C, Turner S R, Krogh K B, Johansen K S, Dupree P. Development and application of a high throughput carbohydrate profiling technique for analyzing plant cell wall polysaccharides and carbohydrate active enzymes. Biotechnol Biofuels, 2013, 6: 94.
doi: 10.1186/1754-6834-6-94 pmid: 23819705
[23] Urbanowicz B R, Peña M J, Ratnaparkhe S, Avci U, Backe J, Steet H F, Foston M, Li H, O’Neill M A, Ragauskas A J, et al. 4-O-methylation of glucuronic acid in Arabidopsis glucuronoxylan is catalyzed by a domain of unknown function family 579 protein. Proc Natl Acad Sci USA, 2012, 109: 14253-14258.
doi: 10.1073/pnas.1208097109 pmid: 22893684
[24] Jensen J K, Kim H, Cocuron J C, Orler R, Ralph J, Wilkerson C G. The DUF579 domain containing proteins IRX15 and IRX15-L affect xylan synthesis in Arabidopsis. Plant J, 2011, 66: 387-400.
[25] Brown D, Wightman R, Zhang Z, Gomez L D, Atanassov I, Bukowski J P, Tryfona T, McQueen-Mason S J, Dupree P, Turner S. Arabidopsis genes IRREGULAR XYLEM (IRX15) and IRX15L encode DUF579-containing proteins that are essential for normal xylan deposition in the secondary cell wall. Plant J, 2011, 66: 401-413.
[26] 刘新红, 邓力超, 曲亮, 惠荣奎, 李莓. 油菜的多用途利用及产业发展建议. 湖南农业科学, 2018, (5): 100-103.
Liu X H, Deng L C, Qu L, Hui R K, Li M. Multipurpose utilization of rape and suggestions on development of rape industry. Hunan Agric Sci, 2018, (5): 100-103 (in Chinese with English abstract).
[27] Chalhoub B, Denoeud F, Liu S Y, Parkin I A P, Tang H B, Wang X Y, Chiquet J, Belcram H, Tong C B, Samans B, et al. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome. Science, 2014, 345: 950-953.
doi: 10.1126/science.1253435 pmid: 25146293
[28] Zhu Y, Wu N, Song W, Yin G, Qin Y, Yan Y, Hu Y. Soybean (Glycine max) expansin gene superfamily origins: segmental and tandem duplication events followed by divergent selection among subfamilies. BMC Plant Biol, 2014, 14: 93.
doi: 10.1186/1471-2229-14-93 pmid: 24720629
[29] Chen C, Wu Y, Li J, Wang X, Zeng Z, Xu J, Liu Y, Feng J, Chen H, He Y, et al. TBtools-II: a “one for all, all for one” bioinformatics platform for biological big-data mining. Mol Plant, 2023, 16: 1733-1742.
[30] Livak K J, Schmittgen T D. Analysis of relative gene expression data using real-time quantitative PCR and the 2 (-Delta Delta C(T)) Method. Methods, 2001, 25: 402-408.
doi: 10.1006/meth.2001.1262 pmid: 11846609
[31] 陈吴钧, 刘江栋, 蒋凯旋, 王幼平, 蒋金金. 甘蓝型油菜BnKNOX基因家族的鉴定与分析. 作物学报, 2023, 49: 2991-3006.
doi: 10.3724/SP.J.1006.2023.34027
Chen W J, Liu J D, Jiang K X, Wang Y P, Jiang J J. Identification and analysis of BnKNOX gene family in Brassica napus. Acta Agron Sin, 2023, 49: 2991-3006 (in Chinese with English abstract).
[32] Cai X, Chang L, Zhang T, Chen H, Zhang L, Lin R, Liang J, Wu J, Freeling M, Wang X. Impacts of allopolyploidization and structural variation on intraspecific diversification in Brassica rapa. Genome Biol, 2021, 22: 166.
doi: 10.1186/s13059-021-02383-2 pmid: 34059118
[1] 郭腾达, 崔梦杰, 陈琳杰, 韩锁义, 郭敬坤, 吴晨迪, 付留洋, 黄冰艳, 董文召, 张新友. 花生磷脂酰肌醇转运蛋白基因AhSFH的克隆及其响应黄曲霉菌侵染的表达特征分析[J]. 作物学报, 2025, 51(6): 1489-1500.
[2] 夏琦, 郭滢, 王坤美, 王思忆, 巨建业, 彭雅雯, 刘忠松, 夏石头. 甘蓝型油菜种子和种皮中水杨酸含量与原花色素积累的关系研究[J]. 作物学报, 2025, 51(5): 1189-1197.
[3] 陆雯佳, 汪军成, 姚立蓉, 张宏, 司二静, 杨轲, 孟亚雄, 李葆春, 马小乐, 王化俊. 大麦PRX基因家族全基因组鉴定及其干旱胁迫下的表达分析[J]. 作物学报, 2025, 51(5): 1198-1214.
[4] 周恩强, 缪亚梅, 周瑶, 姚梦楠, 赵娜, 王永强, 朱宇翔, 薛冬, 李宗迪, 石宇欣, 李波, 汪凯华, 顾春燕, 王学军, 魏利斌. 基于种子发育转录组的豌豆bZIP基因家族分析及种子发育候选基因的鉴定[J]. 作物学报, 2025, 51(4): 914-931.
[5] 潘炬忠, 韦萍, 朱德平, 邵胜雪, 陈珊珊, 韦雅倩, 高维维. 水稻转录因子OsERF104的克隆和功能研究[J]. 作物学报, 2025, 51(4): 900-913.
[6] 王晓琳, 刘忠松, 康雷, 杨柳. 甘蓝型油菜角果长度和每角粒数基因定位以及角果皮转录组动态分析[J]. 作物学报, 2025, 51(4): 888-899.
[7] 张琴, 戴成, 马朝芝. 生长素响应报告基因转化甘蓝型油菜及各组织GUS动态信号分析[J]. 作物学报, 2025, 51(3): 667-675.
[8] 郭冰, 秦家范, 李娜, 宋梦瑶, 王黎明, 李君霞, 马小倩. 谷子SHMT基因家族全基因组鉴定与表达分析[J]. 作物学报, 2025, 51(3): 586-5897.
[9] 孙程明, 周晓婴, 陈锋, 张维, 王晓东, 彭琦, 郭月, 高建芹, 胡茂龙, 付三雄, 张洁夫. 长链非编码RNA (lncRNA)在甘蓝型油菜分枝角度调控中的功能分析与预测[J]. 作物学报, 2025, 51(3): 559-567.
[10] 徐林珊, 郜耿东, 王宇, 王家星, 杨吉招, 武亚瑞, 张宵寒, 常影, 李真, 谢雄泽, 龚德平, 王晶, 葛贤宏. 甘蓝型油菜漆酶基因家族成员表达模式及与茎秆抗折力的关联分析[J]. 作物学报, 2025, 51(1): 134-148.
[11] 李嘉欣, 黄莹, 吴潞梅, 赵伦, 易斌, 马朝芝, 涂金星, 沈金雄, 傅廷栋, 文静. 甘蓝型油菜BnaSLY1基因进化分析及功能研究[J]. 作物学报, 2025, 51(1): 44-57.
[12] 祁稼民, 许春苗, 肖斌. 马铃薯TIFY基因家族的全基因组鉴定及表达分析[J]. 作物学报, 2024, 50(9): 2297-2309.
[13] 杨煜琛, 靳雅荣, 骆金婵, 祝鑫, 李葳航, 贾纪原, 王小珊, 黄德均, 黄琳凯. 珍珠粟WD40基因家族鉴定及表达特征分析[J]. 作物学报, 2024, 50(9): 2219-2236.
[14] 何丹丹, 舒亚洲, 周海连, 吴松果, 魏晓双, 杨明冲, 李波, 吴正丹, 韩世健, 杨娟, 王继斌, 王令强. OsRPTA18参与调控水稻叶片倾角的功能[J]. 作物学报, 2024, 50(8): 1934-1947.
[15] 刘震, 陈丽敏, 李志涛, 朱金勇, 王玮璐, 齐喆颖, 姚攀锋, 毕真真, 孙超, 白江平, 刘玉汇. 马铃薯ARM基因家族的全基因组鉴定及表达分析[J]. 作物学报, 2024, 50(6): 1451-1466.
Viewed
Full text


Abstract

Cited
  Shared   
  Discussed   
No Suggested Reading articles found!
京ICP备15008789号-2