生物技术通报 ›› 2024, Vol. 40 ›› Issue (8): 129-141.doi: 10.13560/j.cnki.biotech.bull.1985.2024-0179
杨巍1,2(), 赵丽芬1,2,3, 唐兵1,2, 周麟笔1,2, 杨娟4, 莫传园1,2, 张宝会1,2, 李飞1,2, 阮松林5, 邓英1,2()
收稿日期:
2024-02-24
出版日期:
2024-08-26
发布日期:
2024-07-31
通讯作者:
邓英,女,博士,研究员,硕士生导师,研究方向:蔬菜遗传育种与栽培;E-mail: 87928883@qq.com作者简介:
杨巍,男,硕士,助理研究员,研究方向:蔬菜遗传育种与栽培;E-mail: yangwei139@sina.cn
基金资助:
YANG Wei1,2(), ZHAO Li-fen1,2,3, TANG Bing1,2, ZHOU Lin-bi1,2, YANG Juan4, MO Chuan-yuan1,2, ZHANG Bao-hui1,2, LI Fei1,2, RUAN Song-lin5, DENG Ying1,2()
Received:
2024-02-24
Published:
2024-08-26
Online:
2024-07-31
摘要:
【目的】SRO基因家族是植物特有的一类转录因子,在植物生长发育与胁迫响应中具有重要作用,研究芥菜SRO基因家族,为解析芥菜SRO基因功能与遗传改良提供理论依据。【方法】利用生物信息学鉴定油用芥菜与菜用芥菜基因组中的SRO基因家族成员,运用TBtools、MEGA、Cytoscape、NCBI、STRING、EggNOG等软件与数据库进行理化性质、序列特征、进化关系、调控网络等分析以及RT-qPCR分析盐胁迫下的表达模式。【结果】两种类型芥菜SRO基因家族成员数量存在差异,并分属A与B两大类,其中A类SRO蛋白含有WWE、PARP及RST结构域,而B类蛋白则缺少WWE结构域,SRO基因启动子区域含有多种非生物胁迫响应与激素响应的顺式作用元件,microRNA-BjuSRO-靶基因构建复杂调控网络,参与了细胞凋亡、根系形态建成、免疫应答、异源刺激的细胞反应、对活性氧的反应等生物学过程,油用芥菜BjuOSRO基因与甘蓝SRO基因具有较近的进化关系,RT-qPCR结果显示,在盐胁迫下BjuVA1a、BjuVA1e、BjuVA2a、BjuVA3a、BjuVB1b、BjuVA2a显著上调表达。【结论】芥菜SRO基因家族具有功能多样性,BjuVA1a、BjuVA1e、BjuVA2a、BjuVA3a、BjuVB1b、BjuVA2a与盐胁迫响应密切相关,可作为培育耐盐型芥菜新品种的候选基因。
杨巍, 赵丽芬, 唐兵, 周麟笔, 杨娟, 莫传园, 张宝会, 李飞, 阮松林, 邓英. 芥菜SRO基因家族全基因组鉴定与表达分析[J]. 生物技术通报, 2024, 40(8): 129-141.
YANG Wei, ZHAO Li-fen, TANG Bing, ZHOU Lin-bi, YANG Juan, MO Chuan-yuan, ZHANG Bao-hui, LI Fei, RUAN Song-lin, DENG Ying. Genome-wide Identification and Expression Analysis of the SRO Gene Family in Brassica juncea L.[J]. Biotechnology Bulletin, 2024, 40(8): 129-141.
基因名称Gene name | 基因ID Gene ID | 正向引物Forward primer(5'-3') | 反向引物Reverse primer(5'-3') |
---|---|---|---|
BjuVA1a | BjuVA05G09830.1 | CACTAAGTCACGCCGAGGAG | CTCTCCACCCACACCAAGTC |
BjuVA1e | BjuVA09G34200.1 | AAACATCGAGGGGACGCAAA | AATGCTCCCCCAACTCCAAG |
BjuVA2a | BjuVB03G32070.1 | ATGTAGGCCGCTTTTCCAGT | AACGTTTGCATCCCCTCGAT |
BjuVA3a | BjuVA08G09520.1 | ACCCAGGATCCTCAAGGTGT | CTCATCTTGCAGCTTTCCGC |
BjuVA4a | BjuVB07G38920.1 | GCGCTTATGAGACTCGCTCT | TCGCCCTCCTCGTAGATCAT |
BjuVB1a | BjuVB03G28110.1 | TCACAACGAGAGCCAAGCAT | AGCCAACGTACCAAGCGTAT |
BjuVB1b | BjuVA07G14180.1 | TCGATCCACTCTCCTCCTCC | GGAGAGGAAACACGTGGTGA |
BjuVB2a | BjuVB04G02010.1 | CGCCGTGGAGAAAACAGAGT | AGAGCATTATCCGGGGAGAGA |
ACT7 | NM_121018.4 | GGAATCGCTGACCGTATGAG | ACCCTCCAATCCAGACACTG |
表1 BjuSROs 实时荧光定量PCR 分析所用引物
Table 1 Primer sequences used in quantitative real-time PCR analysis of BjuSROs
基因名称Gene name | 基因ID Gene ID | 正向引物Forward primer(5'-3') | 反向引物Reverse primer(5'-3') |
---|---|---|---|
BjuVA1a | BjuVA05G09830.1 | CACTAAGTCACGCCGAGGAG | CTCTCCACCCACACCAAGTC |
BjuVA1e | BjuVA09G34200.1 | AAACATCGAGGGGACGCAAA | AATGCTCCCCCAACTCCAAG |
BjuVA2a | BjuVB03G32070.1 | ATGTAGGCCGCTTTTCCAGT | AACGTTTGCATCCCCTCGAT |
BjuVA3a | BjuVA08G09520.1 | ACCCAGGATCCTCAAGGTGT | CTCATCTTGCAGCTTTCCGC |
BjuVA4a | BjuVB07G38920.1 | GCGCTTATGAGACTCGCTCT | TCGCCCTCCTCGTAGATCAT |
BjuVB1a | BjuVB03G28110.1 | TCACAACGAGAGCCAAGCAT | AGCCAACGTACCAAGCGTAT |
BjuVB1b | BjuVA07G14180.1 | TCGATCCACTCTCCTCCTCC | GGAGAGGAAACACGTGGTGA |
BjuVB2a | BjuVB04G02010.1 | CGCCGTGGAGAAAACAGAGT | AGAGCATTATCCGGGGAGAGA |
ACT7 | NM_121018.4 | GGAATCGCTGACCGTATGAG | ACCCTCCAATCCAGACACTG |
图1 BjuSRO基因结构分析 A:BjuSRO蛋白保守基序分析;B:BjuSRO基因结构分析;C:BjuSRO蛋白保守基序logo
Fig. 1 Structure analysis of BjuSRO gene A: Conserved motif analysis of BjuSRO protein. B: Structure analysis of BjuSRO gene. C: Conserved motif logo of BjuSRO protein
图2 BjuSRO蛋白结构域分析 A:SRO蛋白分类示意图;B:代表性BjuSRO蛋白3D结构图;C:BjuSRO蛋白PARP结构域序列比对;D:A类BjuSRO蛋白WWE结构域序列比对; E:BjuSRO蛋白SRT结构域序列比对
Fig. 2 Domain analysis of BjuSRO protein A: Schematic diagram of SRO protein classification. B: 3D structure diagram of representative BjuSRO protein. C: PARP domain sequence alignment of BjuSRO protein. D: WWE domain sequence alignment of class A BjuSRO protein. E: SRT domain sequence alignment of BjuSRO protein
图4 Bju-miRNA与BjuSRO基因互作网络图 菱形表示Bju-miRNA;圆形表示油用芥菜BjuOSRO基因;八边形表示菜用芥菜BjuVSRO基因
Fig. 4 Network diagram of interaction between Bju-miRNA and BjuSRO gene Diamonds indicate Bju-miRNAs; circles indicate BjuOSRO gene of oilseed mustard; octagon indicate BjuVSRO gene of vegetable mustard
图6 BjuRSO蛋白互作分析网络图 八边形表示菜用芥菜SRO蛋白;三角形表示其他蛋白
Fig. 6 Network diagram of BjuRSO protein interaction analysis Octagon indicate SRO proteins of vegetable mustard; triangle indicate other proteins
图7 SRO基因家族进化树分析 圆形表示拟南芥SRO蛋白;五角形表示油用芥菜SRO蛋白;三角形表示菜用芥菜SRO蛋白
Fig. 7 Phylogenetic tree analysis of SRO gene family Circle indicates SRO proteins of Arabidopsis; pentagon indicate SRO proteins of oilseed mustard; triangle indicate SRO proteins of vegetable mustard
图8 SRO基因共线性分析 A:油用芥菜BjuOSRO基因共线性分析;B:菜用芥菜BjuVSRO基因共线性分析;图A和图B中的红线标记A类SRO基因,绿线标记B类SRO基因;C:芥菜SRO直系同源基因对Ka/Ks分析;D:油用芥菜与多物种SRO基因共线性分析(Bol:甘蓝;Bra:大白菜;Lag:丝瓜;Csa:黄瓜;Sol:番茄;Sme:茄子;Pvu:菜豆;Phv:豇豆)
Fig. 8 Collinearity analysis of SRO gene A: Collinear analysis of BjuOSRO gene in oil mustard. B: Collinear analysis of BjuVSRO gene in vegetable mustard. Red line marks class A SRO gene, and green line marks class B SRO gene in Fig. A and B. C: Ka/Ks analysis of SRO homologous genes in mustard. D: Collinearity analysis of SRO gene between oil mustard and multi species(Bol: Cabbage; Bra: Chinese cabbage; Lag: loofah; Csa: cucumber; Sol: tomato; Sme: eggplant; Pvu: kidney beans; Phv: cowpea)
图9 不同时间盐胁迫下芥菜根系BjuSRO基因的相对表达量 不同小写字母表示差异显著(P < 0.05)
Fig. 9 Relative expressions of BjuSRO gene in mustard root system under salt stress at different times Different lowercase letters indicate significant differences(P<0.05)
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