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马铃薯ARM基因家族的全基因组鉴定及表达分析

刘震1，陈丽敏2，李志涛2，朱金勇2，王玮璐2，齐喆颖2，姚攀锋1，毕真真2，孙超2，白江平3，刘玉汇1,*   

  1. 1甘肃农业大学省部共建干旱生境作物学国家重点实验室，甘肃兰州 730070；2 甘肃农业大学农学院，甘肃兰州 730070；3甘肃省教育厅，甘肃兰州 730030
  • 收稿日期:2023-07-14 修回日期:2024-01-12 接受日期:2024-01-12 网络出版日期:2024-02-19
  • 基金资助:
    本研究由甘肃省科技计划资助项目(22JR5RA870，22JR5RA834)，财政部和农业农村部国家现代农业产业技术体系建设项目(CARS-09-P14)，甘肃省科技重大专项(22ZD6NA009)，中央引导地方科技发展资金项目(23ZYQJ304)，省部共建干旱生境作物学国家重点实验室开放基金课题(GSCS-2021-Z02)，甘肃农业大学“伏羲人才”计划项目(Gaufx-02Y04)和甘肃农业大学公招博士科研启动基金项目(GAU-KYQD-2020-11)资助。

Genome-wide identification and expression analysis of ARM gene family in potato (Solanum tuberosum L.)

LIU Zhen1, CHEN Li-Min2, LI Zhi-Tao2, ZHU Jin-Yong2, WANG Wei-Lu2, QI Zhe-Ying2, YAO Pan-Feng1, BI Zhen-Zhen2, SUN Chao2, BAI Jiang-Ping3,LIU Yu-Hui1,*   

  1. 1 State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, Gansu, China; 2 College of Agronomy, Gansu Agricultural University, Lanzhou 730070, Gansu, China; 3 Department of Education of Gansu Province, Lanzhou 730030, Gansu, China
  • Received:2023-07-14 Revised:2024-01-12 Accepted:2024-01-12 Published online:2024-02-19
  • Supported by:
    This study was supported by the Science and Technology Program of Gansu Province (22JR5RA870, 22JR5RA834), the China Agriculture Research System of MOF and MARA (CARS-09-P14), the Major S&T Special Projects of Gansu Province (22ZD6NA009), the Central government guidance for local scientific and technological development projects (23ZYQJ304), the State Key Laboratory of Aridland Crop Science of China (GSCS-2021-Z02), the Fuxi Talent Project of Gansu Agricultural University (Gaufx-02Y04), and the Scientific Research Startup Funds for Openly-recruited Doctors Agricultural University (GAU-KYQD-2020-11).

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摘要：

ARM蛋白重复序列(Armadillo repeats)广泛存在于高等植物中，它们参与多种细胞过程，如信号转导、核转运以及对多种生物/非生物胁迫的响应。本研究在马铃薯(Solanum tuberosum L.)全基因组水平下鉴定出了54个马铃薯ARM基因家族成员(StARMs)，它们不均匀的分布在12条染色体上。根据其蛋白结构和系统发育特征，将54个StARMs分为3个亚家族。片段重复事件在马铃薯ARM基因家族的扩展中起主要作用。共线性分析发现，StARMs与番茄(Solanum lycopersicum)、拟南芥(Arabidopsis)、甘蓝(Brassica oleracea)、水稻(Oryza sativa)、玉米(Zea mays)分别有51对、17对、25对、6对和10对直系同源基因，这些基因均在纯化选择下进化。RNA-seq数据分析发现，4个StARM基因在匍匐茎中特异表达，2个StARM基因在根和心皮中特异表达，1个StARM基因在块茎中特异表，还有一些StARM基因参与了马铃薯对生物/非生物胁迫的响应。此外，本研究对3个不同颜色马铃薯块茎组织(薯皮和薯肉)进行了RNA-seq测序，分析了54个StARMs在不同颜色马铃薯块茎组织中的表达模式，并利用qPCR分析了StARMs 在3个不同颜色块茎杂交子代薯肉中的相对表达量，筛选出了4个可能参与马铃薯块茎花色素苷生物合成的候选基因。本研究为进一步了解StARM基因家族的特征，深入分析StARM基因在马铃薯抵御生物/非生物胁迫和调控块茎花色素苷生物合成中的功能提供了理论依据。

关键词: 马铃薯, ARM基因家族, 生物/非生物胁迫, 花色素苷生物合成, 表达分析

Abstract:

The armadillo repeats (Armadillo repeats) are widely distributed in higher plants and are involved in a variety of cellular processes such as signal transduction, nuclear transport, and the response to various biotic/abiotic stresses. In this study, 54 potato ARM gene family members (StARMs) were identified at the genome-wide level of potato (Solanum tuberosum L.), and they were unevenly distributed on 12 chromosomes. Based on their protein structure and phylogenetic characteristics, 54 StARMs were divided into three subfamilies. Segmental duplication events play a major role in the expansion of potato StARM gene family. Collinearity analysis showed that there were 51, 17, 25, 6, and 10 orthologous gene pairs between StARMs and tomato, Arabidopsis, cabbage, rice, and maize, respectively, which evolved under purification selection. RNA-seq data analysis showed that four StARMs genes were specifically expressed in the stolon, two StARMs were specifically expressed in the root and carpel, and one StARM gene was specifically expressed in the tuber. Some StARM genes were involved in potato response to biotic/abiotic stresses. In addition, we performed RNA-seq on three different colored potato tuber tissues (skin and flesh) and analyzed the relative expression pattern of 54 StARMs genes in different colored potato tuber tissues and the StARMs in potato flesh in three different colored potatoes by qPCR. Four candidate genes that may be involved in anthocyanin biosynthesis in potato tubers were screened. This study provides a theoretical basis for further understanding the characteristics of the StARM gene family and further analyzing the function of the StARM gene in potato resistance to biotic/abiotic stresses and regulation of anthocyanin biosynthesis in tubers.

Key words: potato, ARM gene family, biotic/abiotic stress, anthocyanin biosynthesis, the relative expression pattern

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