Biotechnology Bulletin ›› 2023, Vol. 39 ›› Issue (2): 24-34.doi: 10.13560/j.cnki.biotech.bull.1985.2022-0557
Previous Articles Next Articles
LI Kai-hang(), WANG Hao-chen, CHENG Ke-xin, YANG Yan, JIN Yi, HE Xiao-qing()
Received:
2022-05-07
Online:
2023-02-26
Published:
2023-03-07
LI Kai-hang, WANG Hao-chen, CHENG Ke-xin, YANG Yan, JIN Yi, HE Xiao-qing. Genetic Mechanisms of Plant-microbiome Interaction by Genome-wide Association Analysis Study[J]. Biotechnology Bulletin, 2023, 39(2): 24-34.
Fig. 1 Plant genotype differences affecting the microbial interaction network at the rhizosphere and phyllo-sphere Plants with different genotype gather different microbiome at the rhizosphere and phyllosphere, and the microbiome form a complex network through interaction
Fig. 2 Studying plant-microbiome interactions by network mapping A: Selecting the samples to be collected. B: Isolation of host-associated microbial DNA in different niches. C: OTU and genotype data by sequencing, and measuring plant traits. D: Quantifying microbial networks. E: Calculating microbial network properties by mathematical models and regarding them as phenotypic data. F: Identifying hub taxa. G: Screening significant QTLs by network mapping. H: Excavating hub QTLs by Bayesian networks. I: Quantifying the effect of microbiome on plants traits under the influence of plant genes by path analysis
物种 Species | 基因 Gene | 功能 Function | 生态位 Niche | 参考 Reference |
---|---|---|---|---|
拟南芥Arabidopsis thaliana | CAD1, MIN7 FLS2 ERF CERK1(mfec) | 维持叶际微生物组稳定 | 叶际Phyllosphere | [ |
拟南芥Arabidopsis thaliana | AT2G3671,AT4G13210,AT5G26810,TERPENE SYNTHASE 10 | 负责防御和细胞壁完整性的植物位点 | 叶际Phyllosphere | [ |
拟南芥Arabidopsis thaliana | RPM1,RPS5,RPS2,AtABCG36 | 抗丁香假单胞菌 | 叶际Phyllosphere | [ |
拟南芥Arabidopsis thaliana | RRS1/RPS4,SSL4 | 抗青枯病菌 | 叶际Phyllosphere | [ |
拟南芥Arabidopsis thaliana | MYB72,BGLU42 | 诱导系统抗性 | 叶际Phyllosphere | [ [ |
拟南芥Arabidopsis thaliana | ADA2B, HAL3A等 | 促进植物生长、抗病 | 叶际Phyllosphere | [ |
拟南芥Arabidopsis thaliana | PHR1 | 维持体内磷酸平衡 | 根际Rhizosphere | [ |
拟南芥Arabidopsis thaliana | TMK3,IBR1B等 | 促进拟南芥根系发育、抵抗生物与非生物胁迫 | 根际Rhizosphere | [ |
拟南芥Arabidopsis thaliana | BGLU42 | 诱导系统抗性和铁吸收重要调节因子 | 根际Rhizosphere | [ |
拟南芥Arabidopsis thaliana | F6’H1, PDR9 | 用于合成香豆素并转运到根际中来召集微生物组 | 根际Rhizosphere | [ |
拟南芥Arabidopsis thaliana | FERONIA | 通过调节活性氧来控制根际微生物中的假单胞菌 | 根际Rhizosphere | [ |
拟南芥Arabidopsis thaliana | FERONIA | 召集有益微生物 | 根际Rhizosphere | [ |
拟南芥Arabidopsis thaliana | CYP71A27 | 编码细胞色素P450,缺失会导致根际硫酸盐酶活性降低,假单胞菌对植物促生作用减弱 | 根际Rhizosphere | [ |
玉米Zea mays L. | AGPv3, GRMZM2G031545 | 作为管家基因参与蛋白表达,并普遍出现在所有组织中 | 叶际Phyllosphere | [ |
水稻 Oryza sativa L. | NRT1.1B | 与根系微生物组成和氮素利用有关 | 根际Rhizosphere | [ |
番茄Lycopersicon esculentum Miller | HY5 | 调节菌根共生 | 根际Rhizosphere | [ |
高粱 Sorghum bicolor(Linn.)Moench | RGA2,CHAF1A,SAD5,EXO70B1,ANKRD52,UBA5,IDD16,NHL6,GCAL2 | 它们表现出很强的根特异性活性,包括γ碳酸酐酶样2、假定性β-1,4木聚糖内切酶和抗病蛋白RGA2 | 根际Rhizosphere | [ |
大麦 Hordeum vulgare Linn. | QRMC-3HS,NLR | 植物特异性免疫系统的受体,激活植物的第二层免疫系统,抵御病原菌的侵染。 | 根际Rhizosphere | [ |
Table 1 Plant genes associated with the microbiome
物种 Species | 基因 Gene | 功能 Function | 生态位 Niche | 参考 Reference |
---|---|---|---|---|
拟南芥Arabidopsis thaliana | CAD1, MIN7 FLS2 ERF CERK1(mfec) | 维持叶际微生物组稳定 | 叶际Phyllosphere | [ |
拟南芥Arabidopsis thaliana | AT2G3671,AT4G13210,AT5G26810,TERPENE SYNTHASE 10 | 负责防御和细胞壁完整性的植物位点 | 叶际Phyllosphere | [ |
拟南芥Arabidopsis thaliana | RPM1,RPS5,RPS2,AtABCG36 | 抗丁香假单胞菌 | 叶际Phyllosphere | [ |
拟南芥Arabidopsis thaliana | RRS1/RPS4,SSL4 | 抗青枯病菌 | 叶际Phyllosphere | [ |
拟南芥Arabidopsis thaliana | MYB72,BGLU42 | 诱导系统抗性 | 叶际Phyllosphere | [ [ |
拟南芥Arabidopsis thaliana | ADA2B, HAL3A等 | 促进植物生长、抗病 | 叶际Phyllosphere | [ |
拟南芥Arabidopsis thaliana | PHR1 | 维持体内磷酸平衡 | 根际Rhizosphere | [ |
拟南芥Arabidopsis thaliana | TMK3,IBR1B等 | 促进拟南芥根系发育、抵抗生物与非生物胁迫 | 根际Rhizosphere | [ |
拟南芥Arabidopsis thaliana | BGLU42 | 诱导系统抗性和铁吸收重要调节因子 | 根际Rhizosphere | [ |
拟南芥Arabidopsis thaliana | F6’H1, PDR9 | 用于合成香豆素并转运到根际中来召集微生物组 | 根际Rhizosphere | [ |
拟南芥Arabidopsis thaliana | FERONIA | 通过调节活性氧来控制根际微生物中的假单胞菌 | 根际Rhizosphere | [ |
拟南芥Arabidopsis thaliana | FERONIA | 召集有益微生物 | 根际Rhizosphere | [ |
拟南芥Arabidopsis thaliana | CYP71A27 | 编码细胞色素P450,缺失会导致根际硫酸盐酶活性降低,假单胞菌对植物促生作用减弱 | 根际Rhizosphere | [ |
玉米Zea mays L. | AGPv3, GRMZM2G031545 | 作为管家基因参与蛋白表达,并普遍出现在所有组织中 | 叶际Phyllosphere | [ |
水稻 Oryza sativa L. | NRT1.1B | 与根系微生物组成和氮素利用有关 | 根际Rhizosphere | [ |
番茄Lycopersicon esculentum Miller | HY5 | 调节菌根共生 | 根际Rhizosphere | [ |
高粱 Sorghum bicolor(Linn.)Moench | RGA2,CHAF1A,SAD5,EXO70B1,ANKRD52,UBA5,IDD16,NHL6,GCAL2 | 它们表现出很强的根特异性活性,包括γ碳酸酐酶样2、假定性β-1,4木聚糖内切酶和抗病蛋白RGA2 | 根际Rhizosphere | [ |
大麦 Hordeum vulgare Linn. | QRMC-3HS,NLR | 植物特异性免疫系统的受体,激活植物的第二层免疫系统,抵御病原菌的侵染。 | 根际Rhizosphere | [ |
[1] |
高贵锋, 褚海燕. 微生物组学的技术和方法及其应用[J]. 植物生态学报, 2020, 44(4): 395-408.
doi: 10.17521/cjpe.2019.0222 |
Gao GF, Chu HY. Techniques and methods of microbiomics and their applications[J]. Chin J Plant Ecol, 2020, 44(4): 395-408.
doi: 10.17521/cjpe.2019.0222 URL |
|
[2] |
Trivedi P, Leach JE, Tringe SG, et al. Plant-microbiome interactions: from community assembly to plant health[J]. Nat Rev Microbiol, 2020, 18(11): 607-621.
doi: 10.1038/s41579-020-0412-1 URL |
[3] |
Müller DB, Vogel C, Bai Y, et al. The plant microbiota: systems-level insights and perspectives[J]. Annu Rev Genet, 2016, 50: 211-234.
pmid: 27648643 |
[4] |
Beilsmith K, Thoen MPM, Brachi B, et al. Genome-wide association studies on the phyllosphere microbiome: embracing complexity in host-microbe interactions[J]. Plant J, 2019, 97(1): 164-181.
doi: 10.1111/tpj.14170 |
[5] | Tabrett A, Horton MW. The influence of host genetics on the microbiome[J]. F1000Res, 2020, 9: F1000 Faculty Rev-F1000 Faculty R84. |
[6] |
Cordovez V, Dini-Andreote F, Carrión VJ, et al. Ecology and evolution of plant microbiomes[J]. Annu Rev Microbiol, 2019, 73: 69-88.
doi: 10.1146/annurev-micro-090817-062524 pmid: 31091418 |
[7] |
Bai B, Liu WD, Qiu XY, et al. The root microbiome: community assembly and its contributions to plant fitness[J]. J Integr Plant Biol, 2022, 64(2): 230-243.
doi: 10.1111/jipb.13226 |
[8] |
Dong WT, Zhu YY, Chang HZ, et al. An SHR-SCR module specifies legume cortical cell fate to enable nodulation[J]. Nature, 2021, 589(7843): 586-590.
doi: 10.1038/s41586-020-3016-z URL |
[9] | Delaux PM, Schornack S. Plant evolution driven by interactions with symbiotic and pathogenic microbes[J]. Science, 2021, 371(6531): eaba6605. |
[10] |
Horton MW, Bodenhausen N, Beilsmith K, et al. Genome-wide association study of Arabidopsis thaliana leaf microbial community[J]. Nat Commun, 2014, 5: 5320.
doi: 10.1038/ncomms6320 URL |
[11] |
Wallace JG, Kremling KA, Kovar LL, et al. Quantitative genetics of the maize leaf microbiome[J]. Phytobiomes J, 2018, 2(4): 208-224.
doi: 10.1094/PBIOMES-02-18-0008-R URL |
[12] |
Deng SW, Caddell DF, Xu G, et al. Genome wide association study reveals plant loci controlling heritability of the rhizosphere microbiome[J]. ISME J, 2021, 15(11): 3181-3194.
doi: 10.1038/s41396-021-00993-z pmid: 33980999 |
[13] | Roman-Reyna V, Pinili D, Borja FN, et al. Characterization of the leaf microbiome from whole-genome sequencing data of the 3000 rice genomes project[J]. Rice(N Y), 2020, 13(1): 72. |
[14] |
He XQ, Zhang Q, Li BB, et al. Network mapping of root-microbe interactions in Arabidopsis thaliana[J]. NPJ Biofilms Microbiomes, 2021, 7(1): 72.
doi: 10.1038/s41522-021-00241-4 URL |
[15] |
Ren DQ, Wang XC, Yang M, et al. A new regulator of seed size control in Arabidopsis identified by a genome-wide association study[J]. New Phytol, 2019, 222(2): 895-906.
doi: 10.1111/nph.15642 URL |
[16] | Lahm H, Jia MW, Dreßen M, et al. Congenital heart disease risk loci identified by genome-wide association study in European patients[J]. J Clin Invest, 2021, 131(2): e141837. |
[17] |
Kurilshikov A, Medina-Gomez C, Bacigalupe R, et al. Large-scale association analyses identify host factors influencing human gut microbiome composition[J]. Nat Genet, 2021, 53(2): 156-165.
doi: 10.1038/s41588-020-00763-1 pmid: 33462485 |
[18] |
Hamonts K, Trivedi P, Garg A, et al. Field study reveals core plant microbiota and relative importance of their drivers[J]. Environ Microbiol, 2018, 20(1): 124-140.
doi: 10.1111/1462-2920.14031 pmid: 29266641 |
[19] |
Rodriguez PA, Rothballer M, Chowdhury SP, et al. Systems biology of plant-microbiome interactions[J]. Mol Plant, 2019, 12(6): 804-821.
doi: S1674-2052(19)30171-6 pmid: 31128275 |
[20] |
Wang XL, Wang MX, Xie XG, et al. An amplification-selection model for quantified rhizosphere microbiota assembly[J]. Sci Bull, 2020, 65(12): 983-986.
doi: 10.1016/j.scib.2020.03.005 pmid: 36659026 |
[21] | 丁兆军, 白洋. 根系发育和微生物组研究现状及未来发展趋势[J]. 中国科学: 生命科学, 2021, 51(10): 1447-1456. |
Ding ZJ, Bai Y. The Current and future studies on plant root development and root microbiota[J]. Sci Sin Vitae, 2021, 51(10): 1447-1456.
doi: 10.1360/SSV-2021-0179 URL |
|
[22] |
Wagner MR, Lundberg DS, del Rio TG, et al. Host genotype and age shape the leaf and root microbiomes of a wild perennial plant[J]. Nat Commun, 2016, 7: 12151.
doi: 10.1038/ncomms12151 pmid: 27402057 |
[23] |
Bakker PAHM, Pieterse CMJ, de Jonge R, et al. The soil-borne legacy[J]. Cell, 2018, 172(6): 1178-1180.
doi: S0092-8674(18)30168-5 pmid: 29522740 |
[24] |
Coller E, Cestaro A, Zanzotti R, et al. Microbiome of vineyard soils is shaped by geography and management[J]. Microbiome, 2019, 7(1): 140.
doi: 10.1186/s40168-019-0758-7 pmid: 31699155 |
[25] |
Mitter B, Brader G, Pfaffenbichler N, et al. Next generation microbiome applications for crop production - limitations and the need of knowledge-based solutions[J]. Curr Opin Microbiol, 2019, 49: 59-65.
doi: S1369-5274(19)30040-2 pmid: 31731227 |
[26] |
de Vries FT, Griffiths RI, Knight CG, et al. Harnessing rhizosphere microbiomes for drought-resilient crop production[J]. Science, 2020, 368(6488): 270-274.
doi: 10.1126/science.aaz5192 pmid: 32299947 |
[27] | Gu SH, Yang TJ, Shao ZY, et al. Siderophore-mediated interactions determine the disease suppressiveness of microbial consortia[J]. mSystems, 2020, 5(3): e00811-e00819. |
[28] |
Tao K, Kelly S, Radutoiu S. Microbial associations enabling nitrogen acquisition in plants[J]. Curr Opin Microbiol, 2019, 49: 83-89.
doi: S1369-5274(19)30059-1 pmid: 31733615 |
[29] |
Zhang JY, Liu YX, Zhang N, et al. NRT1.1B is associated with root microbiota composition and nitrogen use in field-grown rice[J]. Nat Biotechnol, 2019, 37(6): 676-684.
doi: 10.1038/s41587-019-0104-4 pmid: 31036930 |
[30] |
Panke-Buisse K, Poole AC, Goodrich JK, et al. Selection on soil microbiomes reveals reproducible impacts on plant function[J]. ISME J, 2015, 9(4): 980-989.
doi: 10.1038/ismej.2014.196 pmid: 25350154 |
[31] |
Lu T, Ke MJ, Lavoie M, et al. Rhizosphere microorganisms can influence the timing of plant flowering[J]. Microbiome, 2018, 6(1): 231.
doi: 10.1186/s40168-018-0615-0 pmid: 30587246 |
[32] |
Mueller ea, Wisnoski ni, Peralta al, et al. Microbial rescue effects: how microbiomes can save hosts from extinction[J]. Funct Ecol, 2020, 34(10): 2055-2064.
doi: 10.1111/1365-2435.13493 URL |
[33] |
Xu L, Coleman-Derr D. Causes and consequences of a conserved bacterial root microbiome response to drought stress[J]. Curr Opin Microbiol, 2019, 49: 1-6.
doi: S1369-5274(19)30007-4 pmid: 31454709 |
[34] |
Chen T, Nomura K, Wang XL, et al. A plant genetic network for preventing dysbiosis in the phyllosphere[J]. Nature, 2020, 580(7805): 653-657.
doi: 10.1038/s41586-020-2185-0 URL |
[35] |
Gong TY, Xin XF. Phyllosphere microbiota: community dynamics and its interaction with plant hosts[J]. J Integr Plant Biol, 2021, 63(2): 297-304.
doi: 10.1111/jipb.13060 |
[36] |
Xu P, Fan XY, Mao YX, et al. Temporal metabolite responsiveness of microbiota in the tea plant phyllosphere promotes continuous suppression of fungal pathogens[J]. J Adv Res, 2022, 39: 49-60.
doi: 10.1016/j.jare.2021.10.003 pmid: 35777916 |
[37] |
Zhu YG, Xiong C, Wei Z, et al. Impacts of global change on the phyllosphere microbiome[J]. New Phytol, 2022, 234(6): 1977-1986.
doi: 10.1111/nph.17928 URL |
[38] |
Perreault R, Laforest-Lapointe I. Plant-microbe interactions in the phyllosphere: facing challenges of the anthropocene[J]. ISME J, 2022, 16(2): 339-345.
doi: 10.1038/s41396-021-01109-3 URL |
[39] |
Li PD, Zhu ZR, Zhang YZ, et al. The phyllosphere microbiome shifts toward combating melanose pathogen[J]. Microbiome, 2022, 10(1): 56.
doi: 10.1186/s40168-022-01234-x URL |
[40] |
Carrión VJ, Perez-Jaramillo J, Cordovez V, et al. Pathogen-induced activation of disease-suppressive functions in the endophytic root microbiome[J]. Science, 2019, 366(6465): 606-612.
doi: 10.1126/science.aaw9285 pmid: 31672892 |
[41] |
Matsumoto H, Fan XY, Wang Y, et al. Bacterial seed endophyte shapes disease resistance in rice[J]. Nat Plants, 2021, 7(1): 60-72.
doi: 10.1038/s41477-020-00826-5 pmid: 33398157 |
[42] |
Bergelson J, Brachi B, Roux F, et al. Assessing the potential to harness the microbiome through plant genetics[J]. Curr Opin Biotechnol, 2021, 70: 167-173.
doi: 10.1016/j.copbio.2021.05.007 URL |
[43] |
Xiong C, Singh BK, He JZ, et al. Plant developmental stage drives the differentiation in ecological role of the maize microbiome[J]. Microbiome, 2021, 9(1): 171.
doi: 10.1186/s40168-021-01118-6 pmid: 34389047 |
[44] |
Hao QY, Jiang R, Hu MB, et al. Dual phase separation in a two-dimensional driven diffusive system[J]. Phys Lett A, 2017, 381(18): 1543-1547.
doi: 10.1016/j.physleta.2017.03.013 URL |
[45] | Schreckenberg M, Schadschneider A, Nagel K, et al. Discrete stochastic models for traffic flow[J]. Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics, 1995, 51(4): 2939-2949. |
[46] |
Rolfe SA, Griffiths J, Ton J. Crying out for help with root exudates: adaptive mechanisms by which stressed plants assemble health-promoting soil microbiomes[J]. Curr Opin Microbiol, 2019, 49: 73-82.
doi: S1369-5274(19)30057-8 pmid: 31731229 |
[47] |
孙雨, 常晶晶, 田春杰. 作物根际微生物组重组构建技术体系探讨[J]. 生物技术通报, 2020, 36(9): 25-30.
doi: 10.13560/j.cnki.biotech.bull.1985.2020-0796 |
Sun Y, Chang JJ, Tian CJ. Technical systems of reorganization and construction of crop rhizosphere microbiome[J]. Biotechnol Bull, 2020, 36(9): 25-30.
doi: 10.13560/j.cnki.biotech.bull.1985.2020-0796 |
|
[48] |
Venturi V, Bez C. A call to arms for cell-cell interactions between bacteria in the plant microbiome[J]. Trends Plant Sci, 2021, 26(11): 1126-1132.
doi: 10.1016/j.tplants.2021.07.007 pmid: 34334316 |
[49] | Wang ZH, Song Y. Toward understanding the genetic bases underlying plant-mediated “cry for help” to the microbiota[J]. iMeta, 2022, 1(1): e8. |
[50] |
Gao M, Xiong C, Gao C, et al. Disease-induced changes in plant microbiome assembly and functional adaptation[J]. Microbiome, 2021, 9(1): 187.
doi: 10.1186/s40168-021-01138-2 pmid: 34526096 |
[51] |
Liu HW, Li JY, Carvalhais LC, et al. Evidence for the plant recruitment of beneficial microbes to suppress soil-borne pathogens[J]. New Phytol, 2021, 229(5): 2873-2885.
doi: 10.1111/nph.17057 URL |
[52] |
Oyserman BO, Flores SS, Griffioen T, et al. Disentangling the genetic basis of rhizosphere microbiome assembly in tomato[J]. Nat Commun, 2022, 13(1): 3228.
doi: 10.1038/s41467-022-30849-9 pmid: 35710629 |
[53] |
Peiffer JA, Spor A, Koren O, et al. Diversity and heritability of the maize rhizosphere microbiome under field conditions[J]. PNAS, 2013, 110(16): 6548-6553.
doi: 10.1073/pnas.1302837110 pmid: 23576752 |
[54] |
Walters WA, Jin Z, Youngblut N, et al. Large-scale replicated field study of maize rhizosphere identifies heritable microbes[J]. Proc Natl Acad Sci USA, 2018, 115(28): 7368-7373.
doi: 10.1073/pnas.1800918115 pmid: 29941552 |
[55] |
程赛赛, 龚鑫, 薛文凤, 等. 生态进化视角的植物-微生物组互作研究进展[J]. 生物技术通报, 2020, 36(9): 3-13.
doi: 10.13560/j.cnki.biotech.bull.1985.2020-0978 |
Cheng SS, Gong X, Xue WF, et al. Plant-microbiome interactions: an eco-evolutionary perspective[J]. Biotechnol Bull, 2020, 36(9): 3-13. | |
[56] |
Xiong C, Zhu YG, Wang JT, et al. Host selection shapes crop microbiome assembly and network complexity[J]. New Phytol, 2021, 229(2): 1091-1104.
doi: 10.1111/nph.16890 URL |
[57] |
Wagner MR. Prioritizing host phenotype to understand microbiome heritability in plants[J]. New Phytol, 2021, 232(2): 502-509.
doi: 10.1111/nph.17622 pmid: 34287929 |
[58] |
Brachi B, Filiault D, Darme P, et al. Plant genetic effects on microbial hubs impact host fitness in repeated field trials[J]. Proc Natl Acad Sci USA, 2022, 119(30): e2201285119.
doi: 10.1073/pnas.2201285119 pmid: 35867817 |
[59] |
Li KH, Cheng KX, Wang HC, et al. Disentangling leaf-microbiome interactions in Arabidopsis thaliana by network mapping[J]. bioRxiv, 2022. DOI:10.1101/2022.04.05.487248.
doi: 10.1101/2022.04.05.487248 |
[60] |
Tam V, Patel N, Turcotte M, et al. Benefits and limitations of genome-wide association studies[J]. Nat Rev Genet, 2019, 20(8): 467-484.
doi: 10.1038/s41576-019-0127-1 pmid: 31068683 |
[61] | 赵宇慧, 李秀秀, 陈倬, 等. 生物信息学分析方法Ⅰ: 全基因组关联分析概述[J]. 植物学报, 2020, 55(6): 715-732. |
Zhao YH, Li XX, Chen Z, et al. An overview of genome-wide association studies in plants[J]. Chin Bull Bot, 2020, 55(6): 715-732. | |
[62] |
Wang HR, Xu X, Vieira FG, et al. The power of inbreeding: NGS-based GWAS of rice reveals convergent evolution during rice domestication[J]. Mol Plant, 2016, 9(7): 975-985.
doi: 10.1016/j.molp.2016.04.018 pmid: 27179918 |
[63] |
Yin LL, Zhang HH, Tang ZS, et al. rMVP: a memory-efficient, visualization-enhanced, and parallel-accelerated tool for genome-wide association study[J]. Genomics Proteomics Bioinformatics, 2021, 19(4): 619-628.
doi: 10.1016/j.gpb.2020.10.007 URL |
[64] |
Bartoli C, Roux F. Genome-wide association studies in plant pathosystems: toward an ecological genomics approach[J]. Front Plant Sci, 2017, 8: 763.
doi: 10.3389/fpls.2017.00763 pmid: 28588588 |
[65] |
Stanton-Geddes J, Paape T, Epstein B, et al. Candidate genes and genetic architecture of symbiotic and agronomic traits revealed by whole-genome, sequence-based association genetics in Medicago truncatula[J]. PLoS One, 2013, 8(5): e65688.
doi: 10.1371/journal.pone.0065688 URL |
[66] |
Moeller AH, Li YY, Mpoudi Ngole E, et al. Rapid changes in the gut microbiome during human evolution[J]. Proc Natl Acad Sci USA, 2014, 111(46): 16431-16435.
doi: 10.1073/pnas.1419136111 pmid: 25368157 |
[67] |
Meyer F, Fritz A, Deng ZL, et al. Critical assessment of metagenome interpretation: the second round of challenges[J]. Nat Methods, 2022, 19(4): 429-440.
doi: 10.1038/s41592-022-01431-4 pmid: 35396482 |
[68] |
Durán P, Thiergart T, Garrido-Oter R, et al. Microbial interkingdom interactions in roots promote Arabidopsis survival[J]. Cell, 2018, 175(4): 973-983.e14.
doi: 10.1016/j.cell.2018.10.020 URL |
[69] |
Toju H, Sato H, Yamamoto S, et al. How are plant and fungal communities linked to each other in belowground ecosystems? A massively parallel pyrosequencing analysis of the association specificity of root-associated fungi and their host plants[J]. Ecol Evol, 2013, 3(9): 3112-3124.
doi: 10.1002/ece3.706 pmid: 24101998 |
[70] | Almario J, Jeena G, Wunder J, et al. Root-associated fungal microbiota of nonmycorrhizal Arabis alpina and its contribution to plant phosphorus nutrition[J]. Proc Natl Acad Sci USA, 2017, 114(44): E9403-E9412. |
[71] | Agler MT, Ruhe J, Kroll S, et al. Microbial hub taxa link host and abiotic factors to plant microbiome variation[J]. PLoS Biol, 2016, 14(1): e1002352. |
[72] | Jiang LB, Liu XJ, He XQ, et al. A behavioral model for mapping the genetic architecture of gut-microbiota networks[J]. Gut Microbes, 2021, 13(1): 1820847. |
[73] |
Koprivova A, Schuck S, Jacoby RP, et al. Root-specific camalexin biosynthesis controls the plant growth-promoting effects of multiple bacterial strains[J]. Proc Natl Acad Sci USA, 2019, 116(31): 15735-15744.
doi: 10.1073/pnas.1818604116 pmid: 31311863 |
[74] |
van der Ent S, Verhagen BWM, van Doorn R, et al. MYB72 is required in early signaling steps of rhizobacteria-induced systemic resistance in Arabidopsis[J]. Plant Physiol, 2008, 146(3): 1293-1304.
doi: 10.1104/pp.107.113829 URL |
[75] |
Zamioudis C, Hanson J, Pieterse CMJ. Β-Glucosidase BGLU42 is a MYB72-dependent key regulator of rhizobacteria-induced systemic resistance and modulates iron deficiency responses in Arabidopsis roots[J]. New Phytol, 2014, 204(2): 368-379.
doi: 10.1111/nph.12980 pmid: 25138267 |
[76] |
Castrillo G, Teixeira PJPL, Paredes SH, et al. Root microbiota drive direct integration of phosphate stress and immunity[J]. Nature, 2017, 543(7646): 513-518.
doi: 10.1038/nature21417 URL |
[77] | Stringlis IA, Yu K, Feussner K, et al. MYB72-dependent coumarin exudation shapes root microbiome assembly to promote plant health[J]. PNAS, 2018, 115(22): E5213-E5222. |
[78] |
Song Y, Wilson AJ, Zhang XC, et al. FERONIA restricts Pseudomonas in the rhizosphere microbiome via regulation of reactive oxygen species[J]. Nat Plants, 2021, 7(5): 644-654.
doi: 10.1038/s41477-021-00914-0 pmid: 33972713 |
[79] |
Song Y, Wilson AJ, Zhang X-C, et al. Loss of a plant receptor kinase recruits beneficial rhizosphere-associated Pseudomonas[J]. BioRxiv. 2020. DOI: https://doi.org/10.1101/2020.11.02.364109.
doi: https://doi.org/10.1101/2020.11.02.364109 |
[80] |
Ge SB, He LQ, Jin LJ, et al. Light-dependent activation of HY5 promotes mycorrhizal symbiosis in tomato by systemically regulating strigolactone biosynthesis[J]. New Phytol, 2022, 233(4): 1900-1914.
doi: 10.1111/nph.17883 URL |
[81] |
Escudero-Martinez C, Coulter M, Alegria Terrazas R, et al. Identifying plant genes shaping microbiota composition in the barley rhizosphere[J]. Nat Commun, 2022, 13(1): 3443.
doi: 10.1038/s41467-022-31022-y pmid: 35710760 |
[82] |
Liu YX, Qin Y, Bai Y. Reductionist synthetic community approaches in root microbiome research[J]. Curr Opin Microbiol, 2019, 49: 97-102.
doi: 10.1016/j.mib.2019.10.010 URL |
[1] | TENG Shou-zhen, WANG Hai, LIANG Hai-sheng, XIN Hong-jia, LI Sheng-yan, LANG Zhi-hong. Genome-wide Association Study of Chlorophyll Content in Maize Leaves [J]. Biotechnology Bulletin, 2017, 33(4): 98-107. |
[2] | Zhang Yanming, Xing Guofang, Liu Meitao, Liu Xiaodong, Han Yuanhuai. Genome Wide Association Study: Opportunities and Challenges in Genomic Research [J]. Biotechnology Bulletin, 2013, 0(6): 1-6. |
Viewed | ||||||
Full text |
|
|||||
Abstract |
|
|||||