萝卜春化响应相关基因鉴定及表达模式分析

doi:10.3969/j.issn.1004-1524.20220927

浙江农业学报 ›› 2023, Vol. 35 ›› Issue (7): 1626-1637.DOI: 10.3969/j.issn.1004-1524.20220927

萝卜春化响应相关基因鉴定及表达模式分析

陈国户¹(), 李广¹, 温宏伟¹, 尹倩¹, 吴思文¹, 王英¹, 刘雪晴¹, 赵龙龙¹, 桂尚枝¹, 唐小燕¹, 汪承刚¹^,²^,^*()

1.安徽省园艺作物育种工程实验室,安徽农业大学园艺学院,安徽合肥 230036
2.安徽省皖江蔬菜产业技术研究院,安徽马鞍山 238253

收稿日期:2022-06-22 出版日期:2023-07-25 发布日期:2023-08-17
作者简介:陈国户(1983—),男,江苏新沂人,博士,副教授,研究方向为蔬菜种质资源与遗传育种。E-mail:cgh@ahau.edu.cn
通讯作者: *汪承刚,E-mail:cgwang@ahau.edu.cn
基金资助:
安徽省教育厅科学研究项目(YJS20210248);国家自然科学基金(31801853);安徽省高校协同创新项目(GXXT-2021-054)

Genome-wide identification and expression analysis of key genes response to vernalization in radish (Raphanus sativus)

CHEN Guohu¹(), LI Guang¹, WEN Hongwei¹, YIN Qian¹, WU Siwen¹, WANG Ying¹, LIU Xueqing¹, ZHAO Longlong¹, KHAN Afrasyab¹, GUI Shangzhi¹, TANG Xiaoyan¹, WANG Chenggang¹^,²^,^*()

1. Anhui Provincial Engineering Laboratory of Horticultural Crop Breeding, School of Horticulture, Anhui Agricultural University, Hefei 230036, China
2. Wanjiang Vegetable Industrial Technology Institute of Anhui Province, Ma‘anshan 238253, Anhui, China

Received:2022-06-22 Online:2023-07-25 Published:2023-08-17
Contact: WANG Chenggang

摘要/Abstract

摘要：

抽薹开花是十字花科蔬菜最重要的性状之一。秋冬季节低温环境,使萝卜(Raphanus sativus L.)过早完成春化,导致未熟抽薹,严重影响产量与品质。本研究采用多重序列比对及系统进化树构建等生物信息学技术,鉴定出萝卜抽薹开花相关基因272个。对萝卜NHJS1、NHJS2和2#材料不同春化阶段的转录组数据进行重分析,筛选出春化相关基因;再结合META分析技术,共确定萝卜春化响应关键基因25个。利用蛋白质-蛋白质互作网络(PPI)分析了春化响应关键基因之间潜在的互作关系。对富集在春化、冷响应、赤霉素生物合成与信号转导途径上的春化响应关键基因进行了实时荧光定量PCR(qRT-PCR)分析,结果显示,RsGA20ox1、RsAGL18、RsFLC2等基因在萝卜春化响应中发挥着重要作用。研究结果为深入解析萝卜春化分子机制奠定了基础。

关键词: 萝卜, 抽薹开花, 春化响应

Abstract:

Bolting and flowering is an important character of Cruciferous crops. The vernalization would be completed in radish (Raphanus sativus L.) by low temperature environment in autumn and winter, which will be resulting in premature bolting. In this study, 272 flowering related genes were identified by multiple sequence alignment and evolutionary tree analyses. The RNA-Seq sequencing data of radish varieties NHJS1, NHJS2 and 2# were analyzed, and 25 key vernalization responded genes were identified combined with the META analysis. The potential links between these key genes were estimated by the protein-protein interaction (PPI) network analysis. Furthermore, the key genes enriched in vernalization, cold responses, gibberellin biosynthesis and signal transduction pathway were verified by qRT-PCR, suggesting that RsGA20ox1, RsAGL18, RsFLC2 and other genes play important roles in vernalization. These results will lay a foundation for further understanding the molecular mechanism vernalization in radish.

Key words: Raphanus sativus, bolting and flowering, vernalization response

中图分类号:

S632.1

陈国户, 李广, 温宏伟, 尹倩, 吴思文, 王英, 刘雪晴, 赵龙龙, 桂尚枝, 唐小燕, 汪承刚. 萝卜春化响应相关基因鉴定及表达模式分析[J]. 浙江农业学报, 2023, 35(7): 1626-1637.

CHEN Guohu, LI Guang, WEN Hongwei, YIN Qian, WU Siwen, WANG Ying, LIU Xueqing, ZHAO Longlong, KHAN Afrasyab, GUI Shangzhi, TANG Xiaoyan, WANG Chenggang. Genome-wide identification and expression analysis of key genes response to vernalization in radish (Raphanus sativus)[J]. Acta Agriculturae Zhejiangensis, 2023, 35(7): 1626-1637.

图/表 11

表1 qRT-PCR引物

Table 1 Primer sequences used for qRT-PCR

基因名称 Gene name	引物序列 Primer sequences (5'→3')	退火温度 Annealing temperature/℃
RsGI	F:GCATCTGGTGTAAGGATAGAAGTT R:AGGGATCAATCCATAGGCAG	57.0
RsGA3ox2	F:ATGGTGAGTGGACAGTGGTCTTA R:CTTTACTCTTGCTTGCCTCTGC	58.0
RsKS	F:GGCTATGATGTGACTTACGATC R:TGCTTAGTCCACAGACACTGC	58.0
RsPRR5	F:GCCTCTGCTTTCACACGGT R:GCACTTTGAGGTGGTTCAGATA	58.5
RsGID1B	F:ATGCAAGATCATTTCCCCGT R:AGGAGGTTGGTGGAGGTGTG	59.0
RsFLC3	F:GCCTTGCAGGATCTTCAGTCA R:AACGAGGGTGTCCACGCTTA	55.0
RsTEM1	F:ACGACCAACGCTAAAC R:TGGAACATCCTAACGCAAAC	58.0
RsGA2ox1	F:GAGTTGAGCCACTAGGGAAG R:TTCACTACTCTGTCTTTTTTCGG	58.1
RsTOC1	F:GAAGCACTAATCCAGCG R:CAGAGGACTCTCCAATCTTCAAC	59.0
RsFLC2	F:CGGCGATAACTTGGTCAAGA R:AGGGCAGTCTCAAGGTGGTC	59.5
RsPRR9	F:TGTAAGTGGTGCTCAGGCTAAC R:GATTCCACCGATCAAGTCCA	56.0
RsCHE	F:GAGACGGATTCGTATGCCAA R:TAGAAGGCTCGGCTTGACG	60.5
RsCDF1	F:GATGAATTATCCGCAGAGC R:CTTCGTTTCCATACTGTTGC	59.0
RsPHYA	F:CATTGAAGGGTGCTTGGATC R:CTGACCTCCAGATGGTGTAAAGT	57.0
RsPHYB	F:GAGAGGGGACGAGGACAAGA R:GACTATGGACGATTGCTCTGTAGT	56.5
RsGA2ox6	F:TCCCTTCAAGTTCAGTTCGG R:GATTGAGTCGCTACGGACG	55.0
actin	F:TACCGCAAAGAGCAGTTCGTCAGTG R:GAGCGATGGCTGGAACAGTACTTCAG	57.5

图1 萝卜开花相关基因染色体定位

Fig.1 Chromosomal mapping of flowering related genes in radish

图2 基于不同组织转录组数据分析萝卜开花相关基因表达情况图中的色标表示log2(FPKM)值。

Fig.2 Tissue expression pattern of flowering related genes based on transcriptomes of radish The color scale bar of the figure represents log2 transformed FPKM values.

图3 萝卜不同材料、不同春化时间转录组数据相关性分析

Fig.3 Correlation analysis of RNA-Seq data among different radish ls and vernalization time

图4 萝卜春化响应基因鉴定及表达分析 A, 萝卜不同材料、不同春化时间转录组差异表达基因(DEG)分析。B,不同材料差异表达基因韦恩图分析。C,VRG,春化反应相关基因;FRG,开花相关基因,T-DEG,不同材料差异表达基因。D,春化相关基因表达趋势;RT,室温春化开始时;VE,春化处理早期;VL,春化处理后期。

Fig.4 Identification and expression analysis of vernalization responded genes in radish A, Differentially expressed genes (DEG) analysis by RNA-Seq data. B, Ween of DEGs between differential materials. C, VRG, Vernalization responded genes; FRG, Flowering related genes; T-DEG, DEGs between differential materials. D, Expression trend of vernalization related gene (VRG); RT, Room temperature treatment; VE, Early vernalization treatment; VL, Late vernalization treatment.

图5 META分析及春化关键基因的鉴定 A,META分析维恩图;RT,室温春化开始时;VE,春化处理早期;VL,春化处理后期。B,春化关键基因韦恩图;FRG,开花相关基因;VRG,转录组学分析获得的春化响应相关基因;M-DEG,META分析获得的差异表达基因。

Fig.5 META analysis and identification of vernalization key genes A, Venn diagram of META analysis; RT, Room temperature treatment; VE, Early vernalization treatment; VL, Late vernalization treatment. B, Venn diagram of key genes responded vernalization; FRG, Flowering related genes; VRG, Vernalization related genes found by transcriptome analysis; M-DEG, Differentially expressed genes obtained by META-analysis.

图6 春化响应关键基因功能富集分析 A,GO富集分析;B,KEGG富集分析;C,赤霉素生物合成通路。A和B中,第一圈表示富集到的GO条目和KO号,第二圈表示富集到该通路的背景基因,第三圈表示富集到该通路上下调基因数目,第四圈表示富集因子。

Fig.6 Functional enrichment analyses of key genes responded vernalization A, GO enrichment; B, KEGG enrichment; C, The pathway of gibberellin biosynthesis. In A and B, the first circle represents the enriched GO entries and KO numbers, the second circle represents the background genes enriched in this pathway, the third circle represents the number of down-regulated genes enriched in this pathway, and the fourth circle represents the enrichment factor.

图7 萝卜春化响应关键基因PPI网络(A)及春化途径(B)与赤霉素途径(C)关键基因网络红色代表上调基因,蓝色代表下调基因。圆的大小代表连接度高低,圆圈越大表示连接度越高。

Fig.7 PPI networks of key genes responded vernalization (A), vernalization pathway (B) and gibberellin pathway (C) Red represents up-regulated protein/gene and green represents down-regulated protein/gene. The size of the circle represents the degree of connection, and the larger the circle, the more connection it is.

表2 光周期、春化、赤霉素生物合成及信号转导途径上的春化响应关键基因

Table 2 Vernalization response key genes in photoperiod, vernalization, gibberellin biosynthesis and signal transduction pathway

序号	萝卜基因ID Rs gene ID	拟南芥基因ID At gene ID	基因名称 Gene name	注释 Annotation	GO	KEGG
1	Rsa10019598	AT5G62430	RsCDF1	CYCLING DOF FACTOR 1	GO:0050789	K16222
2	Rsa10024990	AT5G10140	RsFLC1	FLOWERING LOCUS C-like	GO:0010219
3	Rsa10036313	AT5G10140	RsFLC2	FLOWERING LOCUS C-like	GO:0010219
4	Rsa10009519	AT4G02780	RsGA1	ENT-COPALYL DIPHOSPHATE SYNTHETASE 1	GO:0009739	K04120
5	Rsa10027754	AT3G63010	RsGID1B	GA INSENSITIVE DWARF1B	GO:0007165	K14493
6	Rsa10036693	AT4G25420	RsGA20ox1	GIBBERELLIN 20-OXIDASE 1	GO:0009937	K05282
7	Rsa10012570	AT1G02400	RsGA2ox6	GIBBERELLIN 2-OXIDASE 6	GO:0009685	K04125
8	Rsa10003234	AT1G80340	RsGA3ox2	GIBBERELLIN 3-OXIDASE 2	GO:0009685	K04124
9	Rsa10001141	AT1G22770	RsGI	GIGANTEA	GO:0009648	K12124
10	Rsa10014915	AT1G79460	RsKS	GA REQUIRING 2/ENT-KAURENE SYNTHASE	GO:0010476	K04121
11	Rsa10018279	AT5G24470	RsPRR5	PSEUDO-RESPONSE REGULATOR 5	GO:0048571	K12130
12	Rsa10009861	AT2G46790	RsPRR9	PSEUDO-RESPONSE REGULATOR 9	GO:0048511	K12128
13	Rsa10040564	AT1G25560	RsTEM1	TEMPRANILLO 1	GO:0009908
14	Rsa10017933	AT5G61380	RsTOC1	PRR1/TOC1	GO:0009648	K12127
15	Rsa10028588	AT1G09570	RsPHYA	PHYTOCHROME A	GO:0009416	K12120
16	Rsa10042572	AT2G18790	RsPHYB	PHYTOCHROME B		K12121
17	Rsa10036371	AT5G08330	RsCHE	CHE	GO:0050789	K16221

图8 富集在光周期、春化、赤霉素生物合成及信号转导途径上的春化关键基因的相对表达量不同小写字母表示差异显著(P<0.05)。

Fig.8 Relative expression levels of vernalization key genes enriched in photoperiod, vernalization, gibberellin biosynthesis and signal transduction pathways Different lowercase letters indicate significant difference (P<0.05).

图9 春化响应关键基因调控萝卜抽薹开花

Fig.9 Vernalization responded key genes regulate bolting and flowering in radish

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萝卜春化响应相关基因鉴定及表达模式分析

Genome-wide identification and expression analysis of key genes response to vernalization in radish (Raphanus sativus)

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