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作物学报 ›› 2024, Vol. 50 ›› Issue (6): 1451-1466.doi: 10.3724/SP.J.1006.2024.34121

• 作物遗传育种·种质资源·分子遗传学 • 上一篇    下一篇

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 接受日期:2024-01-12 出版日期:2024-06-12 网络出版日期:2024-02-19
  • 通讯作者: * 刘玉汇, E-mail: lyhui@gsau.edu.cn
  • 作者简介:E-mail: pepsipyy@126.com
  • 基金资助:
    甘肃省科技计划资助项目(22JR5RA870);甘肃省科技计划资助项目(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);甘肃农业大学公招博士科研启动基金项目(GAU-KYQD-2020-11)

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. 1State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, Gansu, China
    2College of Agronomy, Gansu Agricultural University, Lanzhou 730070, Gansu, China
    3Department of Education of Gansu Province, Lanzhou 730030, Gansu, China
  • Received:2023-07-14 Accepted:2024-01-12 Published:2024-06-12 Published online:2024-02-19
  • Contact: * E-mail: lyhui@gsau.edu.cn
  • Supported by:
    Science and Technology Program of Gansu Province(22JR5RA870);Science and Technology Program of Gansu Province(22JR5RA834);China Agriculture Research System of MOF and MARA(CARS-09-P14);Major S&T Special Projects of Gansu Province(22ZD6NA009);Central government guidance for local scientific and technological development projects(23ZYQJ304);State Key Laboratory of Aridland Crop Science of China(GSCS-2021-Z02);Fuxi Talent Project of Gansu Agricultural University(Gaufx-02Y04);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

图1

3个不同颜色马铃薯品种的块茎表型 新大坪: 白皮白肉; 铃田红美: 红皮红肉; 黑美人: 紫皮紫肉。S代表薯皮, F代表薯肉。不同字母表示P < 0.05水平的显著性差异。"

图2

3个马铃薯杂交子代的块茎表型 S1为块茎形成期, S2为块茎成熟期; Y为黄肉品种, R为红肉品种, P为紫肉品种。"

附表1

qPCR引物序列"

基因名称
Gene name		 正向引物
Forward primer (5°-3°)		 反向引物
Reverse primer (5°-3°)
StEF-1α GGTCGTGTTGAGACTGGTGTGATC GCTTCGTGGTGCATCTCTACAGAC
Soltu01G035340 CCAGATATGATTTGTGGTCCTTTTG CAGGGTGTGGAATCAGTAATGTTCT
Soltu02G015230 ATGGCATCTGCTGCAATTTTCT CAACCCAACATCTGTCAGATCCAC
Soltu02G032560 TGTAACCTGGCAGCGAGTTCTG GCAGCAAGACAATTCTCACGAGTC
Soltu03G004990 ATGCTTCGTAATTCGCCGTCA GGCACCAGCATCTATGATACTTTTC
Soltu04G009290 TGGTTTCGCTAGAAAATTCTCATTC TGGTACAAATTGGACCGGATAGTG
Soltu04G032610 TGGAGACTGAAGTTCAATCGAATTT TATCACTGTTGCAATCGCTGAAA
Soltu06G031430 TGTGTTGCGGAGCCTCATAGC ACTACCTGGTCGTTTGGGTGATTC
Soltu07G016540 GTCTAAGGCACAAACCCTAGACCA CCTGCCAGCGAGAAGTAAAAGACT
Soltu08G026240 CAGCTTACAGAAACGGAACACTTCC GCGGTTTTTGATTTGAAAGAAGC
Soltu11G020370 CTCAAGTTGTTGACTCCAATGTTCG GAGCAATTCCTTAGCAGATTCAAGA

附表2

马铃薯ARM基因家族成员及理化性质分析"

基因ID
Gene ID		 染色体定位
Chromosome
localization
(bp)		 外显子
Exon		 内含子
Intron		 氨基酸长度
Amino acid length
(aa)		 相对分子量
Molecular weight
(kD)		 理论等电点Theoretical isoelectric point 亚家族
分类
Subfamily
cluster
Soltu01G020170 Chr.01 30,143,970-30,150,717 - 10 9 529 58.65 5.13 C2
Soltu01G040470 Chr.01 55,223,708-55,229,173 - 10 9 534 59.07 5.13 C2
Soltu01G031070 Chr.01 438,010-444,508 - 12 11 916 98.09 6.50 C3
Soltu01G010740 Chr.01 79,037,941-79,055,022 + 4 3 818 89.26 5.53 C3
Soltu01G032480 Chr.01 70,856,440-70,871,600 - 1 0 555 59.92 8.90 C2
Soltu01G035340 Chr.01 50,713,909-50,724,362 - 4 3 993 110.63 5.53 C3
Soltu01G050860 Chr.01 58,701,505-58,709,231 + 2 1 653 71.93 6.10 C1
Soltu01G032130 Chr.01 54,289,424-54,297,721 - 19 18 880 97.60 6.42 C1
Soltu01G035640 Chr.01 782,037-787,228 + 1 0 311 33.47 5.84 C3
Soltu02G032560 Chr.02 56,324,108-56,329,652 + 1 0 486 53.47 6.85 C3
Soltu02G015230 Chr.02 40,233,405-40,241,625 - 1 0 724 79.30 8.49 C3
Soltu02G018740 Chr.02 16,606,559-16,610,036 + 1 0 576 63.72 7.03 C2
Soltu02G023810 Chr.02 55,687,773-55,696,671 - 1 0 552 60.44 6.22 C1
Soltu02G026750 Chr.02 64,221,992-64,224,506 - 3 2 373 40.65 5.63 C2
Soltu02G010520 Chr.02 50,159,071-50,164,293 - 3 2 330 36.38 5.82 C2
Soltu02G005840 Chr.02 4,301,877-4,305,373 - 1 0 631 69.44 6.41 C1
Soltu02G007220 Chr.02 5,051,243-5,053,770 - 2 1 377 41.25 5.89 C2
Soltu03G003650 Chr.03 4,055,247-4,059,698 - 2 1 664 73.06 8.53 C1
Soltu03G027770 Chr.03 56,643,739-56,649,254 + 1 0 535 58.83 8.63 C3
Soltu03G026010 Chr.03 2,781,211-2,784,877 + 1 0 600 66.39 8.24 C1
Soltu03G004990 Chr.03 72,282,608-72,287,380 - 2 1 310 33.62 6.36 C2
Soltu04G022240 Chr.04 68,531,733-68,541,389 - 6 5 2120 226.50 5.27 C1
Soltu04G032610 Chr.04 44,072,182-44,075,864 + 2 1 356 37.96 5.92 C3
Soltu04G002630 Chr.04 9,543,436-9,546,506 + 4 3 647 69.90 8.44 C3
Soltu04G037650 Chr.04 721,136-723,844 + 8 7 959 107.06 6.63 C3
Soltu04G019300 Chr.04 46,654,769-46,658,455 + 4 3 488 52.67 6.17 C3
Soltu04G009290 Chr.04 44,283,632-44,286,388 + 2 1 451 48.78 5.65 C3
Soltu05G004720 Chr.05 9,441,561-9,453,160 + 4 3 650 70.58 7.85 C3
Soltu05G008330 Chr.05 29,865,050-29,868,218 + 1 0 685 76.06 8.07 C3
Soltu05G008150 Chr.05 30,635,738-30,637,944 + 1 0 685 76.25 7.45 C3
Soltu05G008220 Chr.05 3,610,488-3,613,859 + 3 2 588 65.09 6.03 C3
Soltu05G001590 Chr.05 3,872,355-3,875,948 + 5 4 1046 117.25 5.86 C3
Soltu06G000080 Chr.06 33,056,989-33,059,510 - 10 9 527 58.59 5.00 C2
Soltu06G034720 Chr.06 74,816,160-74,822,802 + 19 18 709 78.08 5.79 C3
Soltu06G031430 Chr.06 87,386,346-87,388,491 - 4 3 572 62.02 5.59 C3
Soltu06G010080 Chr.06 39,654,170-39,673,090 + 1 0 679 74.43 7.14 C3
Soltu07G016540 Chr.07 37,187,439-37,189,097 - 1 0 569 61.74 8.21 C2
Soltu07G014990 Chr.07 52,407,155-52,409,531 - 2 1 393 42.84 5.52 C2
Soltu07G011050 Chr.07 39,584,532-39,587,890 + 2 1 138 15.01 9.27 C2
Soltu08G010180 Chr.08 4,359,566-4,377,252 - 10 9 529 58.40 5.15 C2
Soltu08G026240 Chr.08 25,399,342-25,401,770 + 19 18 906 99.87 6.85 C1
Soltu09G019780 Chr.09 55,879,333-55,890,916 - 19 18 708 78.34 5.86 C3
Soltu09G021390 Chr.09 44,771,850-44,776,570 - 5 4 744 81.58 6.11 C3
Soltu10G023900 Chr.10 19,369,067-19,371,435 - 11 10 520 56.66 5.36 C2
Soltu11G020370 Chr.11 8,313,930-8,316,243 + 4 3 664 72.58 6.01 C3
Soltu11G004340 Chr.11 8,090,829-8,093,283 + 2 1 480 51.92 5.89 C3
Soltu11G000490 Chr.11 71,963,673-71,973,849 - 2 1 458 48.93 6.29 C3
Soltu11G009750 Chr.11 75,124,289-75,125,823 - 6 5 2133 229.40 5.37 C1
Soltu11G020000 Chr.11 8,222,752-8,224,810 - 9 8 704 75.78 7.73 C3
Soltu11G004370 Chr.11 50,992,861-50,995,959 + 22 21 1081 121.90 6.49 C1
Soltu12G000800 Chr.12 21,277,440-21,282,530 - 4 3 821 89.69 5.92 C3
Soltu12G021220 Chr.12 1,207,881-1,212,427 - 1 0 469 51.13 5.71 C2
Soltu12G006210 Chr.12 5,402,137-5,406,934 - 2 1 358 38.41 5.91 C3
Soltu12G004840 Chr.12 35,005,661-35,007,289 - 4 3 645 72.83 5.45 C3

图3

StARM基因家族的进化关系、基因结构和保守基序分析"

附图1

20个Motif的详细信息"

图4

马铃薯ARM基因家族的基因复制事件"

图5

多物种间ARM基因的共线性分析"

图6

StARM基因在DM马铃薯不同组织部位中的表达"

图7

DM马铃薯中StARM基因在生物/非生物胁迫和激素处理下的表达"

图8

StARM基因在不同颜色块茎组织中的表达"

图9

StARM基因在3个杂交子代块茎薯肉中的相对表达量 S1为块茎形成期, S2为块茎成熟期; Y为黄肉品种, R为红肉品种, P为紫肉品种。数据为3个独立生物重复的平均值(±SE)。条形图上方的不同字母表示P < 0.05时的显著差异。"

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