纳米孔测序技术在马铃薯繁育中的应用研究进展

doi:10.12190/j.issn.2096-1197.2024.04.04

摘要/Abstract

摘要： 纳米孔测序是基于单分子的第三代基因测序（third generation sequencing,TGS）技术,具备无须扩增、便于携带、实时测序、超长读长、可直接测序RNA、检测碱基修饰等特点。近年来,纳米孔测序技术发展迅速,在植物基因组重测序、全基因组学、转录组学、细胞器基因组学、表观转录组学等分子植物育种领域得到广泛应用。文章就纳米孔测序技术在国内外马铃薯繁育中的研究现状和应用前景进行阐述,以期为我国马铃薯产业高质量发展提供新思路。

关键词: 纳米孔测序技术, 马铃薯, 繁育, 应用, 基因测序

Abstract: Nanopore sequencing is the third generation sequencing（TGS） technology based on single molecule. It has the characteristics of no amplification,easy to carry,real-time sequencing,ultra long reading length,direct sequencing of RNA,and detection of base modification. In recent years,nanopore sequencing technology has developed rapidly and has been widely applied in molecular plant breeding fields such as plant genome resequencing,whole genome,transcriptomics,organelle genomics,and epigenetic transcriptomics. The article elaborates on the research status and application prospects of nanopore sequencing technology in potato breeding at home and abroad,in order to provide new ideas for the high-quality development of China′s potato industry.

Key words: Nanopore sequencing technology, Potato, Breeding, Application, Gene sequencing

中图分类号:

Q789

康博洋, 崔丽光, 包珺玮, 杜二小, 梁红伟, 谢锐, 郭斌煜, 姜兰剑, 关潇滢, 韩志刚. 纳米孔测序技术在马铃薯繁育中的应用研究进展[J]. 北方农业学报, 2024, 52(4): 29-37.

KANG Boyang, CUI Liguang, BAO Junwei, DU Erxiao, LIANG Hongwei, XIE Rui, GUO Binyu, JIANG Lanjian, GUAN Xiaoying, HAN Zhigang. Research progress on application of nanopore sequencing technology in potato breeding[J]. Journal of Northern Agriculture, 2024, 52(4): 29-37.

参考文献

[1] DEAMER D,AKESON M,BRANTON D.Three decades of nanopore sequencing[J].Nature Biotechnology,2016,34(5):518-524.
[2] WANG Y H,ZHAO Y,BOLLAS A,et al.Nanopore sequencing technology,bioinformatics and applications[J].Nature Biotechnology,2021,39:1348-1365.
[3] WEN L,TANG F C.Recent advances in single-cell sequencing technologies[J].Precision Clinical Medicine,2022,5(1):pbac002.
[4] KAI S,MATSUO Y,NAKAGAWA S,et al.Rapid bacterial identification by direct PCR amplification of 16S rRNA genes using the MinION^TM nanopore sequencer[J].FEBS Open Bio,2019,9(3):548-557.
[5] IMAI K,TARUMOTO N,MISAWA K,et al.A novel diagnostic method for malaria using loop-mediated isothermal amplification(LAMP)and MinION^TM nanopore sequencer[J].BMC Infectious Diseases,2017,17(1):621.
[6] STUBBS S C B,BLACKLAWS B A,YOHAN B,et al.Assessment of a multiplex PCR and nanopore-based method for dengue virus sequencing in Indonesia[J].Virology Journal,2020,17(1):24.
[7] GRUBAUGH N D,LADNER J T,KRAEMER M U G,et al.Genomic epidemiology reveals multiple introductions of Zika virus into the United States[J].Nature,2017,546:401-405.
[8] BRINKMANN A,UDDIN S,KRAUSE E,et al.Utility of a sequence-independent,single-primer-amplification(SISPA)and nanopore sequencing approach for detection and characterization of tick-borne viral pathogens[J].Viruses,2021,13(2):203.
[9] XU X,PAN S K,CHENG S F,et al.Genome sequence and analysis of the tuber crop potato[J].Nature,2011,475:189-195.
[10] PHAM G M,HAMILTON J P,WOOD J C,et al.Construction of a chromosome-scale long-read reference genome assembly for potato[J].GigaScience,2020,9(9):1-11.
[11] NATASCHA L V,ATE B D V,MICHIEL E D V,et al.Solyntus,the new highly contiguous reference genome for potato(Solanum tuberosum).[J].G3 Genes|Genomes|Genetics,2020,10(10):3489-3495.
[12] ZHOU Q,TANG D,HUANG W,et al.Haplotype-resolved genome analyses of a heterozygous diploid potato[J].Nature Genetics,2020,52:1018-1023.
[13] HOOPES G,MENG X X,HAMILTON J P,et al.Phased,chromosome-scale genome assemblies of tetraploid potato reveal a complex genome,transcriptome,and predicted proteome landscape underpinning genetic diversity[J].Molecular Plant,2022,15(3):520-536.
[14] HARDIGAN M A,CRISOVAN E,HAMILTON J P,et al.Genome reduction uncovers a large dispensable genome and adaptive role for copy number variation in asexually propagated Solanum tuberosum[J].The Plant Cell,2016,28(2):388-405.
[15] LIHODEEVSKIY G A,SHANINA E P.Structural variations in the genome of potato varieties of the Ural selection[J].Agronomy,2021,11(9):1703.
[16] LINDBERG J,LUNDEBERG J.The plasticity of the mammalian transcriptome[J].Genomics,2010,95(1):1-6.
[17] ZAGORSCAK M,PETEK M.A comprehensive guide to potato transcriptome assembly[M]//Methods in Molecular Biology.New York:Springer US,2021:155-192.
[18] NIE T K,WANG D D,MA X H,et al.Analysis of key genes involved in potato anthocyanin biosynthesis based on genomics and transcriptomics data[J].Frontiers in Plant Science,2019,10:603.
[19] BAO Y R,NIE T K,WANG D D,et al.Anthocyanin regulatory networks in Solanum tuberosum L. leaves elucidated via integrated metabolomics,transcriptomics,and StAN1 overexpression[J].BMC Plant Biology,2022,22(1):228.
[20] XIONG J,TANG X H,WEI M Z,et al.Comparative full-length transcriptome analysis by Oxford Nanopore Technologies reveals genes involved in anthocyanin accumulation in storage roots of sweet potatoes(Ipomoea batatas L.)[J].PeerJ,2022,10:e13688.
[21] DUMINIL J,BESNARD G.Utility of the mitochondrial genome in plant taxonomic studies[J].Methods in Molecular Biology.New York,NY:Springer US,2020:107-118.
[22] ZASCAVAGE R R,THORSON K,PLANZ J V.Nanopore sequencing:An enrichment-free alternative to mitochondrial DNA sequencing[J].Electrophoresis,2019,40(2):272-280.
[23] KINKAR L,GASSER R,WEBSTER B,et al.Nanopore sequencing resolves elusive long tandem-repeat regions in mitochondrial genomes[J].International Journal of Molecular Sciences,2021,22(4):1811.
[24] FANG B,LI J L,ZHAO Q,et al.Assembly of the complete mitochondrial genome of Chinese plum(Prunus salicina):Characterization of genome recombination and RNA editing sites[J].Genes,2021,12(12):1970.
[25] LI J H,LI J L,MA Y B,et al.The complete mitochondrial genome of okra(Abelmoschus esculentus):Using nanopore long reads to investigate gene transfer from chloroplast genomes and rearrangements of mitochondrial DNA molecules[J].BMC Genomics,2022,23(1):481.
[26] SANETOMO R,AKAI K,NASHIKI A.Discovery of a novel mitochondrial DNA molecule associated with tetrad pollen sterility in potato[J].BMC Plant Biology,2022,22(1):302.
[27] YANG Z J,NI Y,LIN Z B,et al.De novo assembly of the complete mitochondrial genome of sweet potato(Ipomoea batatas[L.] Lam)revealed the existence of homologous conformations generated by the repeat-mediated recombination[J].BMC Plant Biology,2022,22(1):285.
[28] TAKAMATSU T,BASLAM M,INOMATA T,et al.Optimized method of extracting rice chloroplast DNA for high-quality plastome resequencing and de novo assembly[J].Frontiers in Plant Science,2018,9:266.
[29] YOO M J,JIN D P,LEE H O,et al.Complete plastome of three Korean Asarum(Aristolochiaceae):Confirmation tripartite structure within Korean Asarum and comparative analyses[J].Plants,2021,10(10):2056.
[30] YUE J W,LU Q Q,NI Y,et al.Comparative analysis of the plastid and mitochondrial genomes of Artemisia giraldii Pamp[J].Scientific Reports,2022,12:13931.
[31] ZHOU C X,DUARTE T,SILVESTRE R,et al.Insights into population structure of east African sweetpotato cultivars from hybrid assembly of chloroplast genomes[J].Gates Open Research,2020,2:41.
[32] LIHODEEVSKIY G A,SHANINA E P.The use of long-read sequencing to study the phylogenetic diversity of the potato varieties plastome of the Ural selection[J].Agronomy,2022,12(4):846.
[33] YU X,SHARMA B,GREGORY B D.The impact of epitranscriptomic marks on post-transcriptional regulation in plants[J].Briefings in Functional Genomics,2021,20(2):113-124.
[34] LIANG Z,RIAZ A,CHACHAR S,et al.Epigenetic modifications of mRNA and DNA in plants[J].Molecular Plant,2020,13(1):14-30.
[35] YANG L,PERRERA V,SAPLAOURA E,et al.m⁵C methylation guides systemic transport of messenger RNA over graft junctions in plants[J].Current Biology,2019,29(15):2465-2476.
[36] ZHANG G Y,DIAO S F,SONG Y T,et al.Genome-wide DNA N6-adenine methylation in sea buckthorn(Hippophae rhamnoides L.)fruit development[J].Tree Physiology,2022,42(6):1286-1295.
[37] AKHTER Z,BI Z Z,ALI K,et al.In response to abiotic stress,DNA methylation confers epigenetic changes in plants[J].Plants,2021,10(6):1096.
[38] YU Q,LIU S,YU L,et al.RNA demethylation increases the yield and biomass of rice and potato plants in field trials[J].Nature Biotechnology,2021,39(12):1581-1588.
[39] GLUSHKEVICH A,SPECHENKOVA N,FESENKO I,et al.Transcriptomic reprogramming,alternative splicing and RNA methylation in potato(Solanum tuberosum L.)plants in response to potato virus Y infection[J].Plants,2022,11(5):635.
[40] 罗其友,伦闰琪,高明杰,等.2021—2025年我国马铃薯产业高质量发展战略路径[J].中国农业资源与区划,2022,43(3):37-45.
[41] 徐建飞,金黎平.马铃薯遗传育种研究:现状与展望[J].中国农业科学,2017,50(6):990-1015.
[42] 罗其友,高明杰,张烁,等.中国马铃薯产业国际比较分析[J].中国农业资源与区划,2021,42(7):1-8.
[43] 仲乃琴,蔡冬清,赵盼.我国高原马铃薯种薯产业发展与精准扶贫[J].中国科学院院刊,2020,35(10):1308-1313.
[44] 王旭. 强化科技支撑引领推动农业现代化发展[J].中国畜牧业,2022(3):16-17.
[45] LIEFTING L W,WAITE D W,THOMPSON J R.Application of Oxford Nanopore Technology to plant virus detection[J].Viruses,2021,13(8):1424.
[46] DELLA BARTOLA M,BYRNE S,MULLINS E.Characterization of potato virus Y isolates and assessment of nanopore sequencing to detect and genotype potato viruses[J].Viruses,2020,12(4):478.
[47] MEHETRE G T,LEO V V,SINGH G,et al.Current developments and challenges in plant viral diagnostics:A systematic review[J].Viruses,2021,13(3):412.
[48] MONGER W A,GOODFELLOW H A,BACK E J.First report of Arabis mosaic virus in potato(Solanum tuberosum),identified by nanopore sequencing[J].New Disease Reports,2020,41(1):29.
[49] BAI Y J,HAN S X,GAO Y L,et al.Genetic diversity of potato virus Y in potato production areas in northeast China[J].Plant Disease,2019,103(2):289-297.
[50] DONOSO A,VALENZUELA S.In-field molecular diagnosis of plant pathogens:Recent trends and future perspectives[J].Plant Pathology,2018,67(7):1451-1461.
[51] BRONZATO BADIAL A,SHERMAN D,STONE A,et al.Nanopore sequencing as a surveillance tool for plant pathogens in plant and insect tissues[J].Plant Disease,2018,102(8):1648-1652.