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Acta Agronomica Sinica ›› 2024, Vol. 50 ›› Issue (6): 1451-1466.doi: 10.3724/SP.J.1006.2024.34121

• CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS • Previous Articles     Next Articles

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 Online:2024-06-12 Published: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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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

Fig. 1

Tuber phenotypes of three different colored potato cultivars Xindaping: white skin and white flesh; Lingtianhongmei: red skin and red flesh; Heimeiren: purple skin and purple flesh. S: potato skin, F: potato flesh. Different letters above bars denote significant difference at P < 0.05."

Fig. 2

Tuber phenotype of different colored potato hybrid progenies S1: tuber formation stage; S2: tuber maturity stage; Y: the yellow flesh variety; R: the red flesh variety; P: the purple flesh variety."

Table S1

Primer information for qPCR used in this study"

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

Table S2

Analysis of ARM gene family members and physicochemical properties in potato"

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

Fig. 3

Evolutionary relationship, gene structure, and conserved motif of StARM gene family"

Fig. S1

Details of the 20 motifs"

Fig. 4

Gene duplication events in StARM gene family"

Fig. 5

Collinearity analysis of ARM genes in multiple species"

Fig. 6

StARM gene expressions in different tissues of DM potato"

Fig. 7

Expression profiles of StARM genes under biotic/abiotic stresses and hormone treatments in DM potato"

Fig. 8

Expression profiles of StARM genes in different colored tuber tissues"

Fig. 9

Relative expression pattern of StARM genes in potato flesh of three potato hybrids S1: tuber formation stage; S2: tuber maturity stage; Y: the yellow flesh variety; R: the red flesh variety; P: the purple flesh variety. Data are means±SEs with three independent biological replicates. Different letters above the bars denote significant differences at P < 0.05."

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