Identification of Target Genes of the Potato miR7997 Family and Their Expression Dynamics During Late Blight Infection

doi:10.7668/hbnxb.20195974

Abstract

Abstract:

To investigate the molecular mechanisms of the potato miR7997 family in response to Phytophthora infestans infection,this study analyzed the sequence characteristics,target gene prediction,expression patterns,and stress-responsive expression dynamics of Stu-miR7997 and its targets using the potato cultivar Desiree.The results revealed that the potato miR7997 family comprised three members(Stu-miR7997a/b/c)distributed across two chromosomes,with Stu-miR7997a/b sharing identical mature sequences.All precursor sequences formed canonical stem-loop secondary structures,with minimum folding free energies ranging from -37.00 to -49.50 kcal/mol,and mature sequences were located on the 5' arm.Stu-miR7997c exhibited distinct sequence length and functional element distribution compared to Stu-miR7997a/b.Promoter analysis identified light-responsive,hormone-responsive,transcription factor-binding,and stress defense-related cis-regulatory elements;target prediction identified 19 genes predominantly co-regulated by the miR7997 family.Tissue-specific expression profiling showed that Stu-miR7997a/b were highly expressed in stems,while Stu-miR7997c accumulated predominantly in roots.Upon P.infestans infection,all miR7997 members were significantly downregulated,whereas their target genes-including the transcription factor MYB92 gene,NAD(P)H-quinone oxidoreductase gene,and pectin lyase gene-were markedly upregulated.These findings suggest that the Stu-miR7997 family may indirectly modulate potato disease resistance by negatively regulating target genes.This study provides a theoretical foundation for further exploration of the miR7997 family in potato late blight resistance.

Key words: Potato late blight, miR7997 family, Bioinformatics, Target genes, Expression patterns

CLC Number:

CAO Mengqi, CHI Ming, TANG Da, YANG Hengzhao, CHEN Jingting. Identification of Target Genes of the Potato miR7997 Family and Their Expression Dynamics During Late Blight Infection[J]. Acta Agriculturae Boreali-Sinica, 2025, 40(5): 179-187. doi: 10.7668/hbnxb.20195974.

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References 29

[1]	夏善勇, 牛志敏, 李庆全, 张丽娟, 南向日, 盛万民. 马铃薯晚疫病致病疫霉菌遗传多样性及防治研究进展[J]. 黑龙江农业科学, 2022(12):89-94.doi:10.11942/j.issn1002-2767.2022.12.0089.
	Xia S Y, Niu Z M, Li Q Q, Zhang L J, Nan X R, Sheng W M. Research progress on genetic diversity of Phytophthora infestans in potato late blight and its control[J]. Heilongjiang Agricultural Sciences, 2022(12):89-94.
[2]	马蕾, 王施慧, 刘淑梅, 郎丰庆, 纪复勤, 李利斌, 侯丽霞. 番茄和马铃薯CIPK3基因的鉴定和特征分析[J]. 天津农业科学, 2017, 23(8):1-4.doi:10.3969/j.issn.1006-6500.2017.08.001.
	Ma L, Wang S H, Liu S M, Lang F Q, Ji F Q, Li L B, Hou L X. Analysis on identification and characterization of tomato and potato CIPK3 genes[J]. Tianjin Agricultural Sciences, 2017, 23(8):1-4.
[3]	舒锐, 刘少军, 岳林旭, 焦健, 李燕. 农杆菌介导的马铃薯块茎GUS基因瞬时表达研究[J]. 天津农业科学, 2013, 19(11):1-3.doi:10.3969/j.issn.1006-6500.2013.11.001.
	Shu R, Liu S J, Yue L X, Jiao J, Li Y. Research on the transient expression of GUS gene by Agrobacterium tumefaciens in potato tubers[J]. Tianjin Agricultural Sciences, 2013, 19(11):1-3.
[4]	Carrington J C, Ambros V. Role of microRNAs in plant and animal development[J]. Science, 2003, 301(5631):336-338.doi:10.1126/science.1085242.
[5]	Navarro L, Dunoyer P, Jay F, Arnold B, Dharmasiri N, Estelle M, Voinnet O, Jones J D G. A plant miRNA contributes to antibacterial resistance by repressing auxin signaling[J]. Science, 2006, 312(5772):436-439.doi:10.1126/science.1126088.
[6]	Canto-Pastor A, Santos B A M C, Valli A A, Summers W, Schornack S, Baulcombe D C. Enhanced resistance to bacterial and oomycete pathogens by short tandem target mimic RNAs in tomato[J]. Proceedings of the National Academy of Sciences of the United States of America, 2019, 116(7):2755-2760.doi:10.1073/pnas.1814380116.
[7]	Jiang N, Cui J, Yang G L, He X L, Meng J, Luan Y S. Comparative transcriptome analysis shows the defense response networks regulated by miR482b[J]. Plant Cell Reports, 2019, 38(1):1-13.doi:10.1007/s00299-018-2344-z.
[8]	Kumar A, Farooqi M S, Mishra D C, Kumar S, Rai A, Chaturvedi K K, Lal S B, Sharma A. Prediction of miRNA and identification of their relationship network related to late blight disease of potato[J]. MicroRNA, 2018, 7(1):11-19.doi:10.2174/2211536607666171213123038.
[9]	Kapadia C, Datta R, Mahammad S M, Tomar R S, Kheni J K, Ercisli S. Genome-wide identification,quantification,and validation of differentially expressed miRNAs in eggplant(Solanum melongena L.) based on their response toRalstonia solanacearum infection[J].ACS Omega, 2023, 8(2):2648-2657.doi:10.1021/acsomega.2c07097.
[10]	池明. 采用人造小RNA技术抑制马铃薯多酚氧化酶的研究[D]. 杨凌: 西北农林科技大学, 2014.
	Chi M. Study on inhibition of potato polyphenol oxidase by artificial small RNA technology[D]. Yangling: Northwest A&F University, 2014.
[11]	Ni X M, Tian Z D, Liu J, Song B T, Li J C, Shi X L, Xie C H. StPUB17,a novel potato UND/PUB/ARM repeat type gene,is associated with late blight resistance and NaCl stress[J]. Plant Science, 2010, 178(2):158-169.doi:10.1016/j.plantsci.2009.12.002.
[12]	Dai X B, Zhao P X. psRNATarget:a plant small RNA target analysis server[J]. Nucleic Acids Research, 2011, 39(S2):W155-W159.doi:10.1093/nar/gkr319.
[13]	吴保为. 小麦miR5048及其靶基因TaMAPK1和TaNAK1.2的生物学功能和作用机制探析[D]. 杨凌: 西北农林科技大学, 2023.doi:10.27409/d.cnki.gxbnu.2023.000114.
	Wu B W. Biological functions and mechanisms of miR5048 and its target genes TaMAPK1 and TaNAK1.2 in wheat(Triticum aestivum)[D]. Yangling: Northwest A&F University, 2023.
[14]	Bonnet E, He Y, Billiau K, TAPIR,a web server for the prediction of plant microRNA targets,including target mimics[J]. Bioinformatics, 2010, 26(12):1566-1568.doi:10.1093/bioinformatics/btq233.
[15]	曹丽芳. 湖北海棠Mh-miR827与Mh-miR397b响应病原菌侵染功能研究[D]. 南京: 南京农业大学, 2020.doi:10.27244/d.cnki.gnjnu.2020.001171.
	Cao L F. Study on the function of Mh-miR827 and Mh-miR397b in response to pathogen infection of Malus hupehensis[D]. Nanjing: Nanjing Agricultural University, 2020.
[16]	Baker C C, Sieber P, Wellmer F, Meyerowitz E M. The early extra petals1 mutant uncovers a role for microRNA miR164c in regulating petal number in Arabidopsis[J]. Current Biology, 2005, 15(4):303-315.doi:10.1016/j.cub.2005.02.017.
[17]	黄渺, 宋泽洋, 蔡骏一, 南红, 肇瑾. 辣椒miR169家族在非生物胁迫下的表达及启动子顺式作用元件分析[J]. 西部林业科学, 2023, 52(1):165-174.doi:10.16473/j.cnki.xblykx1972.2023.01.022.
	Huang M, Song Z Y, Cai J Y, Nan H, Zhao J. Analysis on expression under abiotic stress and the promoter cis-acting elements of miR169 family in pepper(Capsicum annuum L.)[J]. Journal of West China Forestry Science, 2023, 52(1):165-174.
[18]	曹焜, 孙宇峰, 张晓艳, 赵越, 边境, 朱浩, 王盼, 韩承伟, 孙凯旋, 王晓楠. 工业大麻miR156基因家族在NaHCO₃胁迫下的表达模式及生物信息学分析[J]. 中国麻业科学, 2024, 46(1):10-15,46.doi:10.3969/j.issn.1671-3532.2024.01.002.
	Cao K, Sun Y F, Zhang X Y, Zhao Y, Bian J, Zhu H, Wang P, Han C W, Sun K X, Wang X N. Expression pattern and bioinformatics analysis of miR156 gene family of industrial hemp under NaHCO₃ stress[J]. Plant Fiber Sciences in China, 2024, 46(1):10-15,46.
[19]	Mallory A C, Dugas D V, Bartel D P, Bartel B. microRNA regulation of NAC-domain targets is required for proper formation and separation of adjacent embryonic,vegetative,and floral organs[J].Current Biology, 2004, 14(12):1035-1046.doi:10.1016/j.cub.2004.06.022.
[20]	Zhang B H, Pan X P, Wang Q L, Cobb G P, Anderson T A. Identification and characterization of new plant microRNAs using EST analysis[J]. Cell Research, 2005, 15(5):336-360.doi:10.1038/sj.cr.7290302.
[21]	刘宝宝, 孟桂智, 刘祖江, 贾晶莹, 段红娟, 马云, 蔡小艳. 苜蓿miR156及其靶基因生物信息学分析[J]. 西南农业学报, 2023, 36(7):1385-1392.doi:10.16213/j.cnki.scjas.2023.7.004.
	Liu B B, Meng G Z, Liu Z J, Jia J Y, Duan H J, Ma Y, Cai X Y. Bioinformatics analysis of alfalfa miR156 and its target genes[J]. Southwest China Journal of Agricultural Sciences, 2023, 36(7):1385-1392.
[22]	Axtell M J, Bartel D P. Antiquity of microRNAs and their targets in land plants[J]. The Plant Cell, 2005, 17(6):1658-1673.doi:10.1105/tpc.105.032185.
[23]	Rahmanian S, Murad R, Breschi A, Zeng W H, Mackiewicz M, Williams B, Davis C A, Roberts B, Meadows S, Moore D, Trout D, Zaleski C, Dobin A, Sei L H, Drenkow J, Scavelli A, Gingeras T R, Wold B J, Myers R M, Guig R, Mortazavi A. Dynamics of microRNA expression during mouse prenatal development[J]. Genome Research, 2019, 29(11):1900-1909.doi:10.1101/gr.248997.119.
[24]	Mittler R, Vanderauwera S, Suzuki N, Miller G, Tognetti V B, Vandepoele K, Gollery M, Shulaev V, ROS signaling:the new wave?[J]. Trends in Plant Science, 2011, 16(6):300-309.doi:10.1016/j.tplants.2011.03.007.
[25]	Yin Z Y, Liu J Z, Zhao H P, Chu X M, Liu H Q, Ding X Y, Lu C C, Wang X Y, Zhao X Y, Li Y, Ding X H. SlMYB1 regulates the accumulation of lycopene,fruit shape,and resistance to Botrytis cinerea in tomato[J].Horticulture Research, 2023, 10(2):uhac282.doi:10.1093/hr/uhac282.
[26]	Zou B H, Jia Z H, Tian S M, Wang X M, Gou Z H, Dong H S. AtMYB44 positively modulates disease resistance to Pseudomonas syringae through the salicylic acid signalling pathway in Arabidopsis[J]. Functional Plant Biology, 2013, 40(3):304-313.doi:10.1071/fp12253.
[27]	Shi H J, Cui R Z, Hu B S, Wang X M, Zhang S P, Liu R X, Dong H S. Overexpression of transcription factor AtMYB44 facilitates Botrytis infection in Arabidopsis[J].Physiological and Molecular Plant Pathology, 2011, 76(2):90-95.doi:10.1016/j.pmpp.2011.06.008.
[28]	Li J, Luan Y S, Zhai J M, Liu P, Xia X Y. Bioinformatic analysis of functional characteristics of miR172 family in tomato[J]. Journal of Northeast Agricultural University(English Edition), 2013, 20(4):19-27.doi:10.1016/S1006-8104(14)60042-8.
[29]	Bellincampi D, Cervone F, Lionetti V. Plant cell wall dynamics and wall-related susceptibility in planta pathogen interactions[J]. Frontiers in Plant Science, 2014, 5:228.doi:10.3389/fpls.2014.00228.

引物名称 Primer name	引物序列(5'—3') Primer sequence(5'—3')
Stu-7997c-RT	CTCAACTGGAGCTAGTTTCGTCGTAGGGCAGTTGAGATTTTTGA
TY-Stu-7997-R	CTGGAGCTAGTTTCGTCGTAGGG
Q-Stu-7997c-F	CCAGCTGGGATATTGCTCGGACTCT
Stu-7997a/b-RT	CTCAACTGGAGCTAGTTTCGTCGTAGGGCAGTTGAGTTTGAAGA
Q-Stu-7997a/b-F	CCAGCTGGGATGCTGCTCGGAC
U6-F	CGGGGACATCCGATAAAA
U6-R	TTGGACCATTTCTCGATTTG
RT-U6	CTCAACTGGAGCTAGTTTCGTCGTAGGGCAGTTGAGTTGGACCA

引物名称 Primer name	引物序列(5'—3') Primer sequence(5'—3')
Stu-7997c-RT	CTCAACTGGAGCTAGTTTCGTCGTAGGGCAGTTGAGATTTTTGA
TY-Stu-7997-R	CTGGAGCTAGTTTCGTCGTAGGG
Q-Stu-7997c-F	CCAGCTGGGATATTGCTCGGACTCT
Stu-7997a/b-RT	CTCAACTGGAGCTAGTTTCGTCGTAGGGCAGTTGAGTTTGAAGA
Q-Stu-7997a/b-F	CCAGCTGGGATGCTGCTCGGAC
U6-F	CGGGGACATCCGATAAAA
U6-R	TTGGACCATTTCTCGATTTG
RT-U6	CTCAACTGGAGCTAGTTTCGTCGTAGGGCAGTTGAGTTGGACCA

基因名称 Gene name	引物序列(5'—3') Primer sequence(5'—3')
Stu-β-tublin	ATGTTCAGGCGCAAGGCTT
	TCTGCAACCGGGTCATTCAT
PGSC0003DMT400054374	TGCAGCTAGCTTGAGGAGAG
	TACTGTTGTGTGGGATCTTGGGA
PGSC0003DMT400003790	AAGCTGCTCAAGAAGAGAGGG
	ACCATAAGTTGGCGAGTGCG
PGSC0003DMT400060373	CCGATGTTGGTATGCAGGTGA
	GTCCAATCCCTCTCGTCCAC
PGSC0003DMT400014983	AAATGCCAAAGAGGTGACGAA
	GCTCCATGCTTGATGCCAA
PGSC0003DMT400039552	GACACGCACCCCTTGACATT
	CACCTGAAATGTGGGCAACT
PGSC0003DMT400026391	TGGCTGAGGCACTTGATGAT
	TTTTGAGCGACGGATGGACG

基因名称 Gene name	引物序列(5'—3') Primer sequence(5'—3')
Stu-β-tublin	ATGTTCAGGCGCAAGGCTT
	TCTGCAACCGGGTCATTCAT
PGSC0003DMT400054374	TGCAGCTAGCTTGAGGAGAG
	TACTGTTGTGTGGGATCTTGGGA
PGSC0003DMT400003790	AAGCTGCTCAAGAAGAGAGGG
	ACCATAAGTTGGCGAGTGCG
PGSC0003DMT400060373	CCGATGTTGGTATGCAGGTGA
	GTCCAATCCCTCTCGTCCAC
PGSC0003DMT400014983	AAATGCCAAAGAGGTGACGAA
	GCTCCATGCTTGATGCCAA
PGSC0003DMT400039552	GACACGCACCCCTTGACATT
	CACCTGAAATGTGGGCAACT
PGSC0003DMT400026391	TGGCTGAGGCACTTGATGAT
	TTTTGAGCGACGGATGGACG

前体miRNA ID Pre-miRNA ID	染色体ID Chr ID	起始 Start	终止 End	长度/nt Length
Stu-MIR7997a	2	1 313 823	1 313 940	118
Stu-MIR7997b	5	3 479 983	3 480 100	118
Stu-MIR7997c	5	266 441	266 560	120

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