WANG Tingshuo,ZHAO Jinjuan,YANG Jinping,et al.The Application of Whole Genome Sequencing Technology in Deciphering Plant Metabolic Pathways[J].Northern Horticulture,2025,(21):133-141.[doi:10.11937/bfyy.20251298]
全基因组测序技术在解析植物代谢通路中的应用
- Title:
- The Application of Whole Genome Sequencing Technology in Deciphering Plant Metabolic Pathways
- 文章编号:
- 1001-0009(2025)21-0133-09
- Keywords:
- whole genome sequencing technology; plant metabolic pathways; environmental stress; agronomic traits; sex determination
- 分类号:
- S 188
- 文献标志码:
- A
- 摘要:
- 全基因组测序技术是现代生物学研究的重要工具,在解析植物代谢通路中发挥了重要的作用。植物代谢通路会关乎植物的生长发育和抗逆性,还关乎许多对人类健康有益的次生代谢产物的合成。该研究综述了全基因组测序技术在解析植物代谢通路中的多方面应用,包括植物抗环境胁迫、农艺性状优化、性别决定机制以及天然产物合成等。
- Abstract:
- Whole genome sequencing technology,as an important tool in modern biological research,plays a crucial role in deciphering plant metabolic pathways.Plant metabolic pathways not only influence plant growth,development,and stress resistance but also directly associate with the synthesis of many secondary metabolites beneficial to human health.This study summarized the diverse applications of whole genome sequencing technology in the analysis of plant metabolic pathways,including plant responses to environmental stress,optimization of agronomic traits,sex determination mechanisms,and the synthesis of natural products.
参考文献/References:
[1]ERB M,KLIEBENSTEIN D J.Plant secondary metabolites as defenses,regulators,and primary metabolites:The blurred functional trichotomy[J].Plant Physiology,2020,184(1):39-52.[2]SINGH A,ROYCHOUDHURY A.Abscisic acid in plants under abiotic stress:Crosstalk with major phytohormones[J].Plant Cell Reports,2023,42(6):961-974.[3]GHORBEL M,BRINI F,SHARMA A,et al.Role of jasmonic acid in plants:The molecular point of view[J].Plant Cell Reports,2021,40(8):1471-1494.[4]ZHAO Y W,WANG C K,HUANG X Y,et al.Anthocyanin stability and degradation in plants[J].Plant Signaling & Behavior,2021,16(12):1987767.[5]GENDRISCH F,ESSER P R,SCHEMPP C M,et al.Luteolin as a modulator of skin aging and inflammation[J].BioFactors,2021,47(2):170-180.[6]DEEPIKA,MAURYA P K.Health benefits of quercetin in age-related diseases[J].Molecules,2022,27(8):2498.[7]ANANDAKUMAR P,KAMARAJ S,VANITHA M K.D-limonene:A multifunctional compound with potent therapeutic effects[J].Journal of Food Biochemistry,2021,45(1):e13566.[8]MA D,HE J,HE D.Chamazulene reverses osteoarthritic inflammation through regulation of matrix metalloproteinases (MMPs) and NF-kβ pathway in in-vitro and in-vivo models[J].Bioscience,Biotechnology,and Biochemistry,2020,84(2):402-410.[9]BOCK D G,CAI Z,ELPHINSTONE C,et al.Genomics of plant speciation[J].Plant Communications,2023,4(5):100599.[10]WANG P,MOORE B M,UYGUN S,et al.Optimising the use of gene expression data to predict plant metabolic pathway memberships[J].New Phytologist,2021,231(1):475-489.[11]VARSHNEY R K,SINHA P,SINGH V K,et al.5Gs for crop genetic improvement[J].Current Opinion in Plant Biology,2020,56:190-196.[12]DORADO G,GLVEZ S,ROSALES T E,et al.Analyzing modern biomolecules:The revolution of nucleic-acid sequencing-review[J].Biomolecules,2021,11(8):1111.[13]RDE B A.Frederick sanger (1918—2013)[J].Nature,2014,27:505.[14]MODI A,VAI S,CARAMELLI D,et al.The illumina sequencing protocol and the NovaSeq 6000 system[J].Methods in Molecular Biology,2021,2242:15-42.[15]RHOADS A,AU K F.PacBio sequencing and its applications[J].Genomics,Proteomics & Bioinformatics,2015,13(5):278-289.[16]PUGH J.The current state of nanopore sequencing[M].New York:Springer US,2023.[17]SONG B,NING W,WEI D,et al.Plant genome resequencing and population genomics:Current status and future prospects[J].Molecular Plant,2023,16(8):1252-1268.[18]ZHANG H,ZHU J,GONG Z,et al.Abiotic stress responses in plants[J].Nature Reviews Genetics,2021,23(2):104-119.[19]APOSTOLOVA E L.Molecular mechanisms of plant defense against abiotic stress[J].International Journal of Molecular Sciences,2023,24(12):10339.[20]ZHANG Y,ZHANG A,LI X,et al.The role of chloroplast gene expression in plant responses to environmental stress[J].International Journal of Molecular Sciences,2020,21(17):6082.[21]ZHAO S,ZHANG Q,LIU M,et al.Regulation of plant responses to salt stress[J].International Journal of Molecular Sciences,2021,22(9):4609.[22]FORNASIERO A,WING R A,RONALD P.Rice domestication[J].Current Biology,2022,32(1):R20-R24.[23]WEI H,WANG X,HE Y,et al.Clock component OsPRR73 positively regulates rice salt tolerance by modulating OsHKT2;1-mediated sodium homeostasis[J].EMBO Journal,2021,40(3):e105086.[24]YU J,ZHU C,XUAN W,et al.Genome-wide association studies identify OsWRKY53 as a key regulator of salt tolerance in rice[J].Nature Communications,2023(14):3550.[25]XIE W,LI X,WANG S,et al.OsWRKY53 promotes abscisic acid accumulation to accelerate leaf senescence and inhibit seed germination by downregulating abscisic acid catabolic genes in rice[J].Frontiers in Plant Science,2022(12):816156.[26]ZHAO H,LI Z,WANG Y,et al.Cellulose synthase-like protein OsCSLD4 plays an important role in the response of rice to salt stress by mediating abscisic acid biosynthesis to regulate osmotic stress tolerance[J].Plant Biotechnology Journal,2022,20(3):468-484.[27]ZHANG Q,LIU Y,JIANG Y,et al.OsASR6 enhances salt stress tolerance in rice[J].International Journal of Molecular Sciences,2022,23(16):9340.[28]ZHU X,LIU T,XU K,et al.The impact of high temperature and drought stress on the yield of major staple crops in northern China[J].Journal of Environmental Management,2022,314:115092.[29]PRADO S A,CABRERA-BOSQUET L,GRAU A,et al.Phenomics allows identification of genomic regions affecting maize stomatal conductance with conditional effects of water deficit and evaporative demand[J].Plant,Cell & Environment,2018,41(2):314-326.[30]WANG Y,SUN T,LI T,et al.A CBL-interacting protein kinase TaCIPK2 confers drought tolerance in transgenic tobacco plants through regulating the stomatal movement[J].PLoS One,2016,11(12):e0167962.[31]LYU X,LI Y,CHEN R,et al.Stomatal responses of two drought-tolerant barley varieties with different ROS regulation strategies under drought conditions[J].Antioxidants,2023,12(4):790.[32]REHMAN H M,KHAN U M,NAWAZ S,et al.Genome wide analysis of family-1 UDP glycosyltransferases in Populus trichocarpa specifies abiotic stress responsive glycosylation mechanisms[J].Genes,2022,13(9):1640.[33]GUI Y,FU G,LI X,et al.Identification and analysis of isoflavone reductase gene family in Gossypium hirsutum L[J].Scientific Reports,2023(13):5703.[34]PU Z,QIN T,WANG Y,et al.Genome-wide analysis of the JAZ gene family in potato and functional verification of StJAZ23 under drought stress[J].International Journal of Molecular Sciences,2025,26(5):2360.[35]DAVIES J P,CHRISTENSEN C A.Developing transgenic agronomic traits for crops:Targets,methods,and challenges[J].Methods in Molecular Biology,2019,1864:343-365.[36]SOTO D C,URIBE-SALAZAR J M,SHEW C J,et al.Genomic structural variation:a complex but important driver of human evolution[J].American Journal of Biological Anthropology,2023,181(Suppl 76):118-144.[37]TANG M,WANG T,ZHANG X.A review of SNP heritability estimation methods[J].Briefings in Bioinformatics,2022,23(3):bbac067.[38]ZHANG L,SHI J,OUYANG J,et al.X-CNV:Genome-wide prediction of the pathogenicity of copy number variations[J].Genome Medicine,2021,13(1):132.[39]VAN DER OOST J,PATINIOS C.The genome editing revolution[J].Trends in Biotechnology,2023,41(3):396-409.[40]QIAN R,ZHOU J H,YANG J,et al.Study progress on molecular marker-assisted breeding of Chinese medicinal materials[J].Zhongguo Zhongyao Zazhi,2020,45(20):4812-4818.[41]SHIKHA K,SHAHI J P,VINAYAN M T,et al.Genome-wide association mapping in maize:Status and prospects[J].3 Biotech,2021,11(5):244.[42]DOSSA E N,SHIMELIS H,SHAYANOWAKO A I T.Genetic diversity analysis of tropical and sub-tropical maize germplasm for Striga resistance and agronomic traits with SNP markers[J].PLoS One,2024,19(8):e0306263.[43]TOMKOWIAK A.Identification of SNP and SilicoDArT markers and characterization of their linked candidate genes associated with maize smut resistance[J].International Journal of Molecular Sciences,2024,25(21):11358.[44]DUAN H,LI J,SUN L,et al.Identification of novel loci associated with starch content in maize kernels by a genome-wide association study using an enlarged SNP panel[J].Molecular Breeding,2023,43(12):91.[45]DAS A K,GOWDA M M,MUTHUSAMY V,et al.Development of maize hybrids with enhanced vitamin-E,vitamin-A,lysine,and tryptophan through molecular breeding[J].Frontiers in Plant Science,2021(12):659381.[46]ZHANG Y,WANG M,LI Z,et al.An overview of detecting gene-trait associations by integrating GWAS summary statistics and eQTLs[J].Science China.Life Sciences,2024,67(6):1133-1154.[47]TIBBS CORTES L,ZHANG Z,YU J.Status and prospects of genome-wide association studies in plants[J].The Plant Genome,2021,14(1):e20077.[48]WANG D,HE Y,NIE L,et al.Integrated IBD analysis,GWAS analysis and transcriptome analysis to identify the candidate genes for white spot disease in maize[J].International Journal of Molecular Sciences,2023,24(12):10005.[49]SHI X,FENG C,QIN H,et al.Identification of QTNs and their candidate genes for boll number and boll weight in upland cotton[J].Genes,2024,15(8):1032.[50]SUBEDI M,BAGWELL J W,LOPEZ B,et al.A genome-wide association study approach to identify novel major-effect quantitative trait loci for end-use quality traits in soft red winter wheat[J].Genes,2024,15(9):1177.[51]LIU Y,SHEN K,YIN C,et al.Genetic basis of geographical differentiation and breeding selection for wheat plant architecture traits[J].Genome Biology,2023,24(1):114.[52]MACQUEEN A H,WHITE J W,LEE R,et al.Genetic associations in four decades of multienvironment trials reveal agronomic trait evolution in common bean[J].Genetics,2020,215(1):267-284.[53]RENNER S S,MLLER N A.Sex determination and sex chromosome evolution in land plants[J].Philosophical Transactions of the Royal Society of London.Series B,Biological Sciences,2022,377(1850):20210210.[54]CHENG Z,SONG W,ZHANG X.Genic male and female sterility in vegetable crops[J].Horticulture Research,2023(10):232.[55]CAREY S,YU Q,HARKESS A.The diversity of plant sex chromosomes highlighted through advances in genome sequencing[J].Genes,2021,12(3):381.[56]ASFAW A,MONDO J M,AGRE P A,et al.Association mapping of plant sex and cross-compatibility related traits in white Guinea yam (Dioscorea rotundata Poir.) clones[J].BMC Plant Biology,2022,22(1):294.[57]LIAO Z,ZHANG T,LEI W,et al.A telomere-to-telomere reference genome of Ficus (Ficus hispida) provides new insights into sex determination[J].Horticulture Research,2024(11):257.[58]SANDERSON B J,FENG G,HU N,et al.Sex determination through X-Y heterogamety in Salix nigra[J].Heredity,2021,126(4):630-639.[59]XUE L,WU H,CHEN Y,et al.Evidences for a role of two Y-specific genes in sex determination in Populus deltoides[J].Nature Communications,2020(11):5893.[60]ZHOU R,MACAYA-SANZ D,SCHMUTZ J,et al.Sequencing and analysis of the sex determination region of Populus trichocarpa[J].Genes,2020,11(8):843.[61]MLLER N A,KERSTEN B,LEITE MONTALVO A P,et al.A single gene underlies the dynamic evolution of poplar sex determination[J].Nature Plants,2020,6(6):630-637.[62]EKIERT H M,SZOPA A.Biological activities of natural products[J].Molecules,2020,25(23):5769.[63]MOL M,KABRA R,SINGH S.Genome modularity and synthetic biology:Engineering systems[J].Progress in Biophysics and Molecular Biology,2018,132:43-51.[64]ZHU X,LIU X,LIU T,et al.Synthetic biology of plant natural products:From pathway elucidation to engineered biosynthesis in plant cells[J].Plant Communications,2021,2(5):100229.[65]XIONG X,GOU J,LIAO Q,et al.The Taxus genome provides insights into paclitaxel biosynthesis[J].Nature Plants,2021,7(8):1026-1036.[66]TAN M,NIU J,PENG D Z,et al.Clone and function verification of the OPR gene in Brassica napus related to linoleic acid synthesis[J].BMC Plant Biology,2022,22(1):192.[67]SHI Y,CHEN Z,SHEN M,et al.Identification and functional verification of the glycosyltransferase gene family involved in flavonoid synthesis in Rubus chingii Hu[J].Plants,2024,13(10):1390.[68]XUE Y,SHAN Y,YAO J L,et al.The transcription factor PbrMYB24 regulates lignin and cellulose biosynthesis in stone cells of pear fruits[J].Plant Physiology,2023,192(3):1997-2014.[69]ALAMI M M,OUYANG Z,ZHANG Y,et al.The current developments in medicinal plant genomics enabled the diversification of secondary metabolites′ biosynthesis[J].International Journal of Molecular Sciences,2022,23(24):15932.[70]JIANG Y,QIAN R,ZHANG W,et al.Composition and biosynthesis of scent compounds from sterile flowers of an ornamental plant Clematis florida cv.‘Kaiser’[J].Molecules,2020,25(7):1711.[71]QIAN Y,TONG J,LIU N,et al.Effect of light on ascorbic acid biosynthesis and bioinformatics analysis of related genes in Chinese chives[J].PLoS One,2024,19(8):e0307527.[72]LIAO W,MEI Z,MIAO L,et al.Comparative transcriptome analysis of root,stem,and leaf tissues of Entada phaseoloides reveals potential genes involved in triterpenoid saponin biosynthesis[J].BMC Genomics,2020,21(1):639.[73]PEA R D L,HODGSON H,LIU J C,et al.Complex scaffold remodeling in plant triterpene biosynthesis[J].Science,2023,379(6630):361-368.
备注/Memo
第一作者简介:王庭硕(2001-),男,硕士研究生,研究方向为中药资源与质量控制。E-mail:19854194372@163.com.责任作者:林慧彬(1962-),女,博士,研究员,现主要从事中药资源与质量控制等研究工作。E-mail:linhuibin68@163.com.基金项目:山东省科技型中小企业创新能力提升工程资助项目(2022TSGC1059,2023TSGC0444);中央本级重大增减支资助项目(2060302)。收稿日期:2025-04-07