马铃薯WOX基因家族的鉴定及在离体再生和非生物胁迫中的表达分析

doi:10.13560/j.cnki.biotech.bull.1985.2023-0947

生物技术通报 ›› 2024, Vol. 40 ›› Issue (3): 170-180.doi: 10.13560/j.cnki.biotech.bull.1985.2023-0947

马铃薯WOX基因家族的鉴定及在离体再生和非生物胁迫中的表达分析

张玉¹(), 石磊¹, 巩檑¹, 聂峰杰¹, 杨江伟³^,⁴, 刘璇¹, 杨文静¹, 张国辉⁵, 颉瑞霞⁵, 张丽¹^,²()

1.宁夏农林科学院农业生物技术研究中心宁夏农业生物技术重点实验室，银川 750002
2.甘肃农业大学农学院，兰州 730070
3.甘肃农业大学生命科学技术学院，兰州 730070
4.甘肃农业大学省部共建干旱生境作物学国家重点实验室，兰州 730070
5.宁夏农林科学院固原分院，固原 756000

收稿日期:2023-10-06 出版日期:2024-03-26 发布日期:2024-04-08
通讯作者: 张丽，女，硕士，副研究员，研究方向：作物生物技术育种；E-mail: lesley119@163.com
作者简介:张玉，女，硕士，研究实习员，研究方向：作物生物技术育种；E-mail: nxzy_work@163.com
基金资助:
国家自然科学基金地区科学基金项目(32260529);宁夏自然科学基金项目(2022AAC03428);宁夏农林科学院对外科技合作专项(DW-X-2023004)

Genome-wide Identification of Potato WOX Gene Family and Its Expression Analysis in in vitro Regeneration and Abiotic Stress

ZHANG Yu¹(), SHI Lei¹, GONG Lei¹, NIE Feng-jie¹, YANG Jiang-wei³^,⁴, LIU Xuan¹, YANG Wen-jing¹, ZHANG Guo-hui⁵, XIE Rui-xia⁵, ZHANG Li¹^,²()

1. Research Center of Agricultural Biotechnology, Ningxia Academy of Agriculture and Forestry Sciences, Ningxia Key Laboratory of Agricultural Biotechnology, Yinchuan 750002
2. Agronomy College, Gansu Agricultural University, Lanzhou 730070
3. College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070
4. State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070
5. Guyuan Branch of Ningxia Academy of Agriculture and Forestry Sciences, Guyuan 756000

Received:2023-10-06 Published:2024-03-26 Online:2024-04-08

摘要/Abstract

摘要：

【目的】 WUSCHE-相关同源盒（WUSCHEL-related homeobox, WOX）基因家族是植物特有的转录因子家族，在植物生长发育、干细胞分化调控、逆境胁迫响应等过程中扮演重要角色。开展马铃薯WOX基因家族鉴定与功能研究，将为马铃薯遗传改良提供优良基因资源与理论依据。【方法】 基于拟南芥、番茄、烟草和水稻WOX蛋白序列，利用HMMER 3.0和BLASTP鉴定马铃薯WOX基因家族成员，使用MCScanX软件分析WOX基因家族成员在马铃薯种内及种间的共线性，并采用邻接法构建系统发育进化树。利用ExPASy、GSDS等软件分析马铃薯WOX基因家族成员理化性质、基因结构、蛋白motif、启动子区域转录因子结合位点。基于PGSC数据库中马铃薯转录组数据，分析StWOXs在不同组织和非生物胁迫下的表达模式；以可能参与离体再生过程的StWOX5作为候选基因，利用实时荧光定量PCR技术分析该基因在具有不同离体再生能力的4个马铃薯品种（系）再生过程中的表达情况。【结果】 鉴定得到11个马铃薯WOX基因家族成员，分布在5条染色体上，分为WUS、中间和古老共3个进化分支，不同分支中StWOXs基因结构、蛋白motif组成、转录因子结合位点类型和数量存在不同程度的差异。表达模式结果表明，马铃薯WOX基因家族成员参与离体再生和非生物胁迫响应，StWOX4/5/11/13在愈伤组织中特异表达，StWUS、StWOX1/3c/4/5/13在甘露醇处理下上调表达，StWOX3a/11在NaCl处理下上调表达，StWOX4/5/13在热胁迫中上调表达，且StWOX5相对表达量与愈伤组织分化率呈正相关。【结论】 不同马铃薯WOX基因具有潜在的功能多样性，StWOX5具有促进马铃薯离体再生分化的作用，参与了非生物胁迫反应。

关键词: 马铃薯, WOX基因家族, 愈伤组织, 基因表达

Abstract:

【Objective】 The WUSCHEL-related homeobox（WOX）gene family is plant-specific, which plays important roles in plant growth and development, regulation of stem cell differentiation, and response to adverse stress. Identification of potato WOX gene family may provide a theoretical basis and gene resources for potato genetic improvement.【Method】 Based on the WOX protein sequences of Arabidopsis thaliana, tomato, tobacco and rice, all members of potato WOX gene family were identified by HMMER 3.0 and BLASTP, MCScanX was used for collinear analysis, and the phylogenetic tree was constructed using neighbor-joining method. Physical and chemical properties, gene structure, protein motif, and transcription factor binding sites of potato WOX members were analyzed by ExPASy, GSDS and other software. Expression patterns of StWOXs were analyzed based on potato transcriptome data from PGSC database. RT-qPCR assay was carried out to analyze relative expression of StWOX5 in four potato varieties（lines）with different in vitro regeneration abilities.【Result】 11 members of potato WOX gene family were identified, distributed on five chromosomes, and classified into three clades, namely WUS, intermediate and ancient, with differences in gene structure, motif composition, transcription factor binding sites. The results showed that members of potato WOX gene family were involved in in vitro regeneration and abiotic stress responses. StWOX4/5/11/13 were specifically expressed in callus, StWUS and StWOX1/3c/4/5/13 were up-regulated under mannitol treatment, StWOX3a/11 were up-regulated under salt treatment, and StWOX4/5/13 were up-regulated under heat stress. The relative expression of StWOX5 was positively correlated with the differentiation rate.【Conclusion】 Different potato WOX genes had potential functional diversity. StWOX5 may promote potato regeneration in vitro and participate in abiotic stress responses.

Key words: Solanum tuberosum L., WOX gene family, callus, gene expression

张玉, 石磊, 巩檑, 聂峰杰, 杨江伟, 刘璇, 杨文静, 张国辉, 颉瑞霞, 张丽. 马铃薯WOX基因家族的鉴定及在离体再生和非生物胁迫中的表达分析[J]. 生物技术通报, 2024, 40(3): 170-180.

ZHANG Yu, SHI Lei, GONG Lei, NIE Feng-jie, YANG Jiang-wei, LIU Xuan, YANG Wen-jing, ZHANG Guo-hui, XIE Rui-xia, ZHANG Li. Genome-wide Identification of Potato WOX Gene Family and Its Expression Analysis in in vitro Regeneration and Abiotic Stress[J]. Biotechnology Bulletin, 2024, 40(3): 170-180.

图/表 9

表1 实时荧光定量PCR引物

Table 1 Primers used in real-time quantitative PCR

基因 Gene	引物序列 Primer sequence（5'-3'）
StWOX5	F: TGCTGAAACTGAAAAGCTTAGACT
StWOX5	R: GGATGATCCATCTCAGCTCCA
EF1α	F: CAAGGATGACCCAGCCAAG
EF1α	R: TTCCTTACCTGAACGCCTGT

表2 马铃薯WOX基因家族成员信息

Table 2 Information of WOX gene family members in S. tuberosum

序号 No.	基因 Gene	基因ID Gene ID	染色体上位置 Position in chromosome	氨基酸数量Number of amino acids	相对分子质量Molecular weight/kD	等电点Isoelectric points	亚细胞定位Subcellular localization
1	StWUS	Soltu.DM.02G023940	chr.02:37 323 370-37 324 685	263	29.8	6.55	细胞核Nuclear
2	StWOX1	Soltu.DM.03G033140	chr.03:56 859 969-56 862 746	391	44.1	6.71	细胞核Nuclear
3	StWOX2	Soltu.DM.06G031390	chr.06:56 294 501-56 295 977	236	26.7	8.61	细胞核Nuclear
4	StWOX3a	Soltu.DM.11G026210	chr.11:46 280 883-46 282 433	213	24.5	9.07	细胞核Nuclear
5	StWOX3b	Soltu.DM.11G026200	chr.11:46 246 409-46 248 855	200	23.1	9.28	细胞核Nuclear
6	StWOX3c	Soltu.DM.06G031020	chr.06:55 970 577-55 972 200	173	20.0	9.97	细胞核Nuclear
7	StWOX4	Soltu.DM.04G033400	chr.04:64 994 427-64 996 252	243	28.0	8.91	细胞核Nuclear
8	StWOX5	Soltu.DM.03G012800	chr.03:34 493 065-34 493 856	157	18.5	5.95	细胞核Nuclear
9	StWOX9	Soltu.DM.02G016680	chr.02:31 173 532-31 175 481	333	37.1	7.33	细胞核Nuclear
10	StWOX11	Soltu.DM.06G028250	chr.06:53 617 232-53 619 413	323	35.6	5.78	细胞核Nuclear
11	StWOX13	Soltu.DM.02G022590	chr.02:36 352 960-36 356 110	275	30.9	5.53	细胞核Nuclear

图1 马铃薯WOX成员共线性分析 A：马铃薯WOX成员种内共线性分析图；B：拟南芥、番茄、水稻、马铃薯WOX种间共线性分析图

Fig. 1 Collinear analysis of potato WOX members A: The collinear analysis of WOX members in S. tuberosum. B: The collinear analysis in different WOX members between Arabidopsis thaliana, S. lycopersicum, Oryza sativa, and S. tuberosum

图2 马铃薯、拟南芥、番茄、烟草、水稻WOX蛋白的系统发育分析

Fig. 2 Phylogenetic analysis of WOX proteins among S. tuberosum, A. thaliana, S. lycopersicum, N. tabacum, and O. sativa

图3 StWOXs基因结构示意图

Fig. 3 Structure of StWOX genes

图4 StWOX蛋白motif分布及其序列标识

Fig. 4 Distribution and sequence logos of motifs in StWOX proteins

图5 StWOXs启动子区域转录因子结合位点预测及数量统计 A：转录因子结合位点预测；B：转录因子结合位点数量统计

Fig. 5 Prediction and numerical statistics of TFBS in the promoter region of StWOXs A: The prediction of TFBS. B: The statistical analysis of TFBS

图6 StWOXs在不同组织部位（A）、干旱和盐胁迫（B）、热胁迫（C）中的表达模式

Fig. 6 Relative expression patterns of StWOXs in different tissues（A）, under drought and salt stresses（B）, and under heat stress（C）

图7 马铃薯不同品种（系）愈伤组织诱导分化及StWOX5的RT-qPCR验证 A：马铃薯不同品种（系）愈伤组织诱导阶段表型；B：马铃薯不同品种（系）愈伤组织诱导率；C：马铃薯不同品种（系）愈伤组织分化阶段表型；D：马铃薯不同品种（系）愈伤组织分化率；E：StWOX5在马铃薯不同品种（系）愈伤组织分化阶段的相对表达量。小写字母表示差异达到显著水平（P<0.05）

Fig. 7 Callus induction and differentiation of different potato varieties（lines）, and RT-qPCR verification of StWOX5 A: Phenotypes of different potato varieties（lines）at the stage of callus induction. B: Callus induction rates in different potato varieties（lines）. C: Phenotypes of different potato varieties（lines）at the stage of callus differentiation. D: Callus differentiation rates in different potato varieties（lines）. E: Relative expressions of StWOX5 in different potato varieties（lines）at the stage of callus differentiation. The lowercase letters indicate that the difference reached a significant level（P<0.05）

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马铃薯WOX基因家族的鉴定及在离体再生和非生物胁迫中的表达分析

Genome-wide Identification of Potato WOX Gene Family and Its Expression Analysis in in vitro Regeneration and Abiotic Stress

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