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作物学报 ›› 2022, Vol. 48 ›› Issue (1): 86-98.doi: 10.3724/SP.J.1006.2022.04285

• 作物遗传育种·种质资源·分子遗传学 • 上一篇    下一篇

马铃薯PIF家族成员鉴定及其对高温胁迫的响应分析

荐红举1,2,3(), 尚丽娜1,2,3(), 金中辉1,2,3, 丁艺1, 李燕1,3, 王季春1,2,3, 胡柏耿4, Vadim Khassanov5, 吕典秋1,2,3,*()   

  1. 1西南大学农学与生物科技学院, 重庆 400715
    2南方山地农业教育部工程研究中心, 重庆 400715
    3薯类生物学与遗传育种重庆市重点实验室, 重庆 400715
    4国家马铃薯工程技术研究中心, 山东德州 253600
  • 收稿日期:2020-12-29 接受日期:2021-04-14 出版日期:2022-01-12 网络出版日期:2021-05-20
  • 通讯作者: 吕典秋
  • 作者简介:荐红举, E-mail: hjjian518@swu.edu.cn
    尚丽娜, E-mail: cxldshanglina@163.com第一联系人：**同等贡献
  • 基金资助:
    国家自然科学基金资助项目(32101659);科技部科技伙伴计划项目(KY201904016);国家重点研发计划项目(2018YFE0127900);西南大学人才引进项目资助(SWU019008);西南大学人才引进项目资助(SWU020009)

Genome-wide identification and characterization of PIF genes and their response to high temperature stress in potato

JIAN Hong-Ju1,2,3(), SHANG Li-Na1,2,3(), JIN Zhong-Hui1,2,3, DING Yi1, LI Yan1,3, WANG Ji-Chun1,2,3, HU Bai-Geng4, Vadim Khassanov5, LYU Dian-Qiu1,2,3,*()   

  1. 1College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
    2State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Chongqing 400715, China
    3Chongqing Key Laboratory of Biology and Genetic Breeding for Tuber and Root Crops, Chongqing 400715, China
    4National Engineering Research Center for Potato, Dezhou 253600, Shandong, China
  • Received:2020-12-29 Accepted:2021-04-14 Published:2022-01-12 Published online:2021-05-20
  • Contact: LYU Dian-Qiu
  • About author:First author contact:** Contributed equally to this work
  • Supported by:
    National Natural Science Foundation of China(32101659);Science and Technology Partnership Program, Ministry of Science and Technology of China(KY201904016);National Key Research and Development Program of China(2018YFE0127900);Talent Introduction Program of Southwest University Project(SWU019008);Talent Introduction Program of Southwest University Project(SWU020009)

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摘要：

植物光敏色素作用因子(phytochrome interacting factors, PIFs)属于碱性-螺旋-环-螺旋(basic helix-loop-helix, bHLH)转录因子家族, 通过将光和温度等外部环境信号与植物体内源信号途径相整合, 进而形成复杂的信号转导网络来精密调控植物的生长发育进程。目前, 关于马铃薯PIF家族基因的研究较少, 鉴定和分析StPIF家族成员有助于进一步提高马铃薯的产量和品质。本研究运用生物信息学方法, 以拟南芥PIF家族成员蛋白序列作为源序列, 通过在马铃薯基因组数据库中进行BlastP分析鉴定出7个StPIFs家族成员, 并对其进行系统进化、染色体分布、复制事件、蛋白理化性质、基因结构、Motif预测、启动子顺式作用元件、基因表达模式以及对高温胁迫的响应分析。结果显示, StPIF家族所有成员均含有Motif 1 (bHLH结构域)、Motif 2 (APB结构域)基序; 在StPIF基因的启动子区域预测到多个参与光响应、激素、干旱、低温、昼夜节律以及防御和应激反应调控元件; 基因表达模式和现蕾期高温胁迫响应分析表明, 家族成员具有明显的组织表达特异性, 基因存在功能分化, 且大部分StPIF成员对生物胁迫和高温等非生物胁迫具有明显响应。以上研究结果极大丰富了我们对StPIF家族的认识, 为进一步探究StPIF基因在马铃薯生长期应对生物胁迫以及在结薯期应对高温等非生物胁迫中发挥的功能奠定了理论基础。

关键词: 马铃薯(Solanum tuberosum L.), PIF家族, 生物信息学, 高温, 表达模式分析

Abstract:

Phytochrome interacting factors (PIFs) belong to the basic helix-loop-helix (bHLH) transcription factor family, which integrates external environmental signals such as light and temperature with plant endogenous signal pathways, and then form a complex signal transduction network to precisely regulate the growth and development of plants. Up to now, there are few studies of PIF family genes in potato. Identification and analysis of StPIF family members will help to further improve the yield and quality of potatoes. In this study, BlastP analysis was performed in the potato genome database using Arabidopsis PIFs family member protein sequences as source sequences and seven StPIFs family members were identified. Systemic evolution, chromosome distribution, replication events, protein physicochemical properties, gene structure, motif prediction, promoter cis-acting elements, gene expression pattern, and the response to high temperature stress were also conducted. These results showed that all members of the StPIFs gene family contain Motif 1 (bHLH domain) and Motif 2 (APB domain); multiple cis-regulatory elements involved in light response, hormones, drought, low temperature, and circadian rhythm as well as defense and stress response regulatory elements were predicted in the promoter regions of the StPIF genes. Results of gene expression patterns and high temperature stress response at budding stage revealed that StPIFs family members had obvious tissue expression specificity, indicating their functional differentiation, and most StPIFs members had obvious responses to biotic stress and abiotic stresses including high temperature. In conclusion, these foundlings greatly enriched the understanding of the members of the StPIF family, and laid a theoretical foundation for further exploring the functions of StPIFs genes in responses to biotic stress and abiotic stress during potato growth period including high temperature at tuber stage.

Key words: potato (Solanum tuberosum L.), PIF family, bioinformatics, high temperature, the relative expression pattern

表1

本研究所用引物"

引物
Primer		 正向序列
Forward sequence (5'-3')		 反向序列
Reverse sequence (5'-3')
ef1α
StPIF1a
StPIF1b
StPIF3
StPIF4
StPIF8		 ATTGGAAACGGATATGCTCCA
GTTTCACACGTACCCGATAATG
GTACTTCGACTGTAGAGATCCG
GAGTTTAGGTATGGGTATGGGG
TGAACTTCCTGTTCCACATCAA
AATCAGTGTGTACCGAGTTG		 TCCTTACCTGAACGCCTGTCA
GAAATGTCACATGTAGTCGTCG
TTTGAATCCACAATCGTCGATG
TACAGCTATTCCTGGATAAGCG
TTCATTAGGATCATAGCCTGGC
CTAACCCATGCATTGCTAAC

表2

马铃薯PIFs家族成员的序列特性"

基因
Gene		 基因编号
Gene ID		 氨基酸数目
Number of amino acids (aa)		 分子量Molecular weight (kD) 等电点Isoelectric point (pI) 位置
Location		 功能域
Functional domains
(Start-End, bp)
StPIF1a PGSC0003DMG400018950 578 62.94 6.42 ch09:45450532-45460120 343-406/bHLH
StPIF1b PGSC0003DMG400014705 515 56.41 5.13 ch06:2038519-2047215 309-372/bHLH
StPIF3 PGSC0003DMG400018280 708 75.83 7.26 ch01:79007967-79013234 450-512/bHLH
StPIF4 PGSC0003DMG401015926 517 57.44 7.09 ch07:42074703-42078252 331-394/bHLH
StPIF7a PGSC0003DMG400024554 437 48.17 6.79 ch03:55395567-55398080 237-298/bHLH
StPIF7b PGSC0003DMG400033087 416 46.81 8.71 ch06:51466651-51468759 195-252/bHLH
StPIF8 PGSC0003DMG400025976 464 50.75 7.62 ch01:70077080-70081427 281-344/bHLH

图1

拟南芥、马铃薯和番茄PIF氨基酸多序列比对 A: APB结构域; B: APA结构域; C: bHLH结构域。"

图2

PIF基因家族系统发育进化树 At: 拟南芥; St: 马铃薯; Sl: 番茄; Os: 水稻; Zm: 玉米。"

图3

马铃薯PIF基因结构和保守基序 Motif: 保守基序; UTR: 非翻译区; CDS: 编码区序列。"

图4

马铃薯PIFs家族成员保守基序"

图5

马铃薯PIF基因家族共线性分析"

图6

马铃薯、拟南芥和番茄PIF基因的共线性分析"

图7

马铃薯StPIF基因启动子中与胁迫反应和植物发育相关的顺式作用元件"

图8

马铃薯PIF启动子序列保守基序"

图9

马铃薯PIF家族成员启动子保守基序"

图10

马铃薯PIF启动子序列结合转录因子"

图11

马铃薯PIF基因对环境胁迫的响应"

图12

高温胁迫下StPIF家族基因在不同组织部位的表达分析"

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