Generic placeholder image

Current Genomics

Editor-in-Chief

ISSN (Print): 1389-2029
ISSN (Online): 1875-5488

Review Article

Plant-microbe Interactions for Sustainable Agriculture in the Postgenomic Era

Author(s): Raj Kishan Agrahari, Prashantee Singh, Hiroyuki Koyama and Sanjib Kumar Panda*

Volume 21, Issue 3, 2020

Page: [168 - 178] Pages: 11

DOI: 10.2174/1389202921999200505082116

Price: $65

Abstract

Plant-microbe interactions are both symbiotic and antagonistic, and the knowledge of both these interactions is equally important for the progress of agricultural practice and produce. This review gives an insight into the recent advances that have been made in the plant-microbe interaction study in the post-genomic era and the application of those for enhancing agricultural production. Adoption of next-generation sequencing (NGS) and marker assisted selection of resistant genes in plants, equipped with cloning and recombination techniques, has progressed the techniques for the development of resistant plant varieties by leaps and bounds. Genome-wide association studies (GWAS) of both plants and microbes have made the selection of desirable traits in plants and manipulation of the genomes of both plants and microbes effortless and less time-consuming. Stress tolerance in plants has been shown to be accentuated by association of certain microorganisms with the plant, the study and application of the same have helped develop stress-resistant varieties of crops. Beneficial microbes associated with plants are being extensively used for the development of microbial consortia that can be applied directly to the plants or the soil. Next-generation sequencing approaches have made it possible to identify the function of microbes associated in the plant microbiome that are both culturable and non-culturable, thus opening up new doors and possibilities for the use of these huge resources of microbes that can have a potential impact on agriculture.

Keywords: Plant-microbe interaction, crop improvement, plant immune response, GWAS, plant growth-promoting bacteria, plant stress management.

Graphical Abstract
[1]
Johansson, J.F.; Paul, L.R.; Finlay, R.D. Microbial interactions in the mycorrhizosphere and their significance for sustainable agriculture. FEMS Microbiol. Ecol., 2004, 48(1), 1-13.
[http://dx.doi.org/10.1016/j.femsec.2003.11.012] [PMID: 19712426]
[2]
Bennett, R.A.; Lynch, J.M. Colonization potential of bacteria in therhizosphere. Curr. Microbiol., 1981, 6, 137-138.
[http://dx.doi.org/10.1007/BF01642386]
[3]
Lindow, S.E.; Brandl, M.T. Microbiology of the phyllosphere. Appl. Environ. Microbiol., 2003, 69(4), 1875-1883.
[http://dx.doi.org/10.1128/AEM.69.4.1875-1883.2003] [PMID: 12676659]
[4]
Smith, K.P.; Goodman, R.M. Host variation for interactions with beneficial plant-associated microbes. Annu. Rev. Phytopathol., 1999, 37, 473-491.
[http://dx.doi.org/10.1146/annurev.phyto.37.1.473] [PMID: 11701832]
[5]
Berg, G.; Krechel, A.; Ditz, M.; Sikora, R.A.; Ulrich, A.; Hallmann, J. Endophytic and ectophytic potato-associated bacterial communities differ in structure and antagonistic function against plant pathogenic fungi. FEMS Microbiol. Ecol., 2005, 51(2), 215-229.
[http://dx.doi.org/10.1016/j.femsec.2004.08.006] [PMID: 16329870]
[6]
Farrar, K.; Bryant, D.; Cope-Selby, N. Understanding and engineering beneficial plant-microbe interactions: plant growth promotion in energy crops. Plant Biotechnol. J., 2014, 12(9), 1193-1206.
[http://dx.doi.org/10.1111/pbi.12279] [PMID: 25431199]
[7]
Nelson, L.M. Plant growth promoting rhizobacteria (PGPR): Prospects for new inoculants. Crop Manag., 2004, 3(1)
[http://dx.doi.org/10.1094/CM-2004-0301-05-RV]
[8]
Bhattacharyya, P.N.; Goswami, M.P.; Bhattacharyya, L.H. Perspective of beneficial microbes in agriculture under changing climatic scenario: a review. J. Phytol., 2016, 8, 26-41.
[http://dx.doi.org/10.19071/jp.2016.v8.3022]
[9]
Singh, J.S.; Pandey, V.C.; Singh, D.P. Efficient soil microorganisms: a new dimension for sustainable agriculture and environmental development. Agric. Ecosyst. Environ., 2011, 140, 339-353.
[http://dx.doi.org/10.1016/j.agee.2011.01.017]
[10]
Glick, B.R. Bacteria with ACC deaminase can promote plant growth and help to feed the world. Microbiol. Res., 2014, 169(1), 30-39.
[http://dx.doi.org/10.1016/j.micres.2013.09.009] [PMID: 24095256]
[11]
Hamilton, C.E.; Bever, J.D.; Labbe, J.; Yang, X.; Yin, H. Mitigating climate change through managing constructed microbial communities in agriculture. Agric. Ecosyst. Environ., 2016, 216, 304-308.
[http://dx.doi.org/10.1016/j.agee.2015.10.006]
[12]
Lugtenberg, B.; Kamilova, F. Plant-growth-promoting rhizobacteria. Annu. Rev. Microbiol., 2009, 63, 541-556.
[http://dx.doi.org/10.1146/annurev.micro.62.081307.162918] [PMID: 19575558]
[13]
Thynne, E.; McDonald, M.C.; Solomon, P.S. Phytopathogen emergence in the genomics era. Trends Plant Sci., 2015, 20(4), 246-255.
[http://dx.doi.org/10.1016/j.tplants.2015.01.009] [PMID: 25682011]
[14]
Withers, S.; Gongora-Castillo, E.; Gent, D.; Thomas, A.; Ojiambo, P.S.; Quesada-Ocampo, L.M. Using next-generation sequencing to develop molecular diagnostics for Pseudoperonospora cubensis, the cucurbit downy mildew pathogen. Phytopathology, 2016, 106(10), 1105-1116.
[http://dx.doi.org/10.1094/PHYTO-10-15-0260-FI] [PMID: 27314624]
[15]
Cai, M.; Qiu, D.; Yuan, T.; Ding, X.; Li, H.; Duan, L.; Xu, C.; Li, X.; Wang, S. Identification of novel pathogen-responsive cis-elements and their binding proteins in the promoter of OsWRKY13, a gene regulating rice disease resistance. Plant Cell Environ., 2008, 31(1), 86-96.
[PMID: 17986178]
[16]
Wang, D.; Pajerowska-Mukhtar, K.; Culler, A.H.; Dong, X. Salicylic acid inhibits pathogen growth in plants through repression of the auxin signaling pathway. Curr. Biol., 2007, 17(20), 1784-1790.
[http://dx.doi.org/10.1016/j.cub.2007.09.025] [PMID: 17919906]
[17]
Olukolu, B.A.; Tracy, W.F.; Wisser, R.; De Vries, B.; Balint-Kurti, P.J. A genome-wide association study for partial resistance to maize common rust. Phytopathology, 2016, 106(7), 745-751.
[http://dx.doi.org/10.1094/PHYTO-11-15-0305-R] [PMID: 27003507]
[18]
Barea, J.M. Future challenges and perspectives for applying microbial biotechnology in sustainable agriculture based on a better understanding of plant-microbiome interactions. J. Soil Sci. Plant Nutr., 2015, 15, 261-282.
[19]
Davison, J. Plant beneficial bacteria. Nat. Biotechnol., 1988, 6, 282-286.
[http://dx.doi.org/10.1038/nbt0388-282]
[20]
Whipps, J.M. Microbial interactions and biocontrol in the rhizosphere. J. Exp. Bot., 2001, 52(Spec Issue), 487-511.
[http://dx.doi.org/10.1093/jxb/52.suppl_1.487] [PMID: 11326055]
[21]
Veresoglou, S.D.; Rillig, M.C. Suppression of fungal and nematode plant pathogens through arbuscular mycorrhizal fungi. Biol. Lett., 2012, 8(2), 214-217.
[http://dx.doi.org/10.1098/rsbl.2011.0874] [PMID: 22012951]
[22]
Smith, K.P.; Handelsman, J.; Goodman, R.M. Genetic basis in plants for interactions with disease-suppressive bacteria. Proc. Natl. Acad. Sci. USA, 1999, 96(9), 4786-4790.
[http://dx.doi.org/10.1073/pnas.96.9.4786] [PMID: 10220371]
[23]
Lugtenberg, B.J.; Chin-A-Woeng, T.F.; Bloemberg, G.V. Microbe-plant interactions: principles and mechanisms. Antonie van Leeuwenhoek, 2002, 81(1-4), 373-383.
[http://dx.doi.org/10.1023/A:1020596903142] [PMID: 12448736]
[24]
Akhond, M.A.Y.; Machray, G.C. Biotech crops: technologies, achievements, and prospects. Euphytica, 2009, 166(1), 47-59.
[http://dx.doi.org/10.1007/s10681-008-9823-1]
[25]
Gust, A.A.; Brunner, F.; Nürnberger, T. Biotechnological concepts for improving plant innate immunity. Curr. Opin. Biotechnol., 2010, 21(2), 204-210.
[http://dx.doi.org/10.1016/j.copbio.2010.02.004] [PMID: 20181472]
[26]
Miller, S.A.; Beed, F.D.; Harmon, C.L. Plant disease diagnostic capabilities and networks. Annu. Rev. Phytopathol., 2009, 47, 15-38.
[http://dx.doi.org/10.1146/annurev-phyto-080508-081743] [PMID: 19385729]
[27]
Adesemoye, A.O.; Torbert, H.A.; Kloepper, J.W. Plant growth-promoting rhizobacteria allow reduced application rates of chemical fertilizers. Microb. Ecol., 2009, 58(4), 921-929.
[http://dx.doi.org/10.1007/s00248-009-9531-y] [PMID: 19466478]
[28]
Adesemoye, A.O.; Kloepper, J.W. Plant-microbes interactions in enhanced fertilizer-use efficiency. Appl. Microbiol. Biotechnol., 2009, 85(1), 1-12.
[http://dx.doi.org/10.1007/s00253-009-2196-0] [PMID: 19707753]
[29]
Haggag, W.M.; Abouziena, H.F.; Abd-El-Kreem, F.; El Habbasha, S. Agriculture biotechnology for management of multiple biotic and abiotic environmental stress in crops. J. Chem. Pharm. Res., 2015, 7(10), 882-889.
[30]
Allwood, J.W.; Clarke, A.; Goodacre, R.; Mur, L.A.J. Dual metabolomics: a novel approach to understanding plant-pathogen interactions. Phytochemistry, 2010, 71(5-6), 590-597.
[http://dx.doi.org/10.1016/j.phytochem.2010.01.006] [PMID: 20138320]
[31]
Abdin, M.Z.; Khan, M.A.; Ali, A.; Alam, P.; Ahmad, A.; Sarwat, M. Signal transduction and regulatory networks in plant-pathogen interaction: a proteomics perspective. Stress Signaling in Plants: Genomics and Proteomics Perspective; Sarwat, M.; Ahmad, A; Abdin, M., Ed.; Springer: New York, 2013, Vol. 1, pp. 69-90.
[http://dx.doi.org/10.1007/978-1-4614-6372-6_4]
[32]
Seo, E.; Choi, D. Choi. Functional studies of transcription factors involved in plant defenses in the genomics era. Brief. Funct. Genomics, 2015, 14(4), 260-267.
[http://dx.doi.org/10.1093/bfgp/elv011] [PMID: 25839837]
[33]
Maciá-Vicente, J.G.; Jansson, H.B.; Talbot, N.J.; Lopez-Llorca, L.V. Real-time PCR quantification and live-cell imaging of endophytic colonization of barley (Hordeum vulgare) roots by Fusarium equiseti and Pochonia chlamydosporia. New Phytol., 2009, 182(1), 213-228.
[http://dx.doi.org/10.1111/j.1469-8137.2008.02743.x] [PMID: 19170898]
[34]
Tshikhudo, P.P.; Ntushelo, K.; Mudau, F.N.; Salehi, B.; Sharifi-Rad, M.; Martins, N.; Martorell, M.; Sharifi-Rad, J. Understanding Camellia sinensis using omics technologies along with endophytic bacteria and environmental roles on metabolism. Appl. Sci. (Basel), 2019, 9(2), 281.
[http://dx.doi.org/10.3390/app9020281]
[35]
Mark, G.L.; Dow, J.M.; Kiely, P.D.; Higgins, H.; Haynes, J.; Baysse, C.; Abbas, A.; Foley, T.; Franks, A.; Morrissey, J.; O’Gara, F. Transcriptome profiling of bacterial responses to root exudates identifies genes involved in microbe-plant interactions. Proc. Natl. Acad. Sci. USA, 2005, 102(48), 17454-17459.
[http://dx.doi.org/10.1073/pnas.0506407102] [PMID: 16301542]
[36]
Bregar, O.; Mandelc, S.; Celar, F.; Javornik, B. Proteome analysis of the plant pathogenic fungus Monilinialaxa showing host specificity. Food Technol. Biotechnol., 2012, 50, 326-333.
[37]
Swarupa, V.; Pavitra, K.; Shivashankara, K.S.; Ravishankar, K.V. Omics-driven approaches in plant-microbe interaction.Microbial inoculants in sustainable agricultural productivity; Singh, D.P.; Singh, H.B.; Prabha, R., Eds.; Springer India:. New Delhi, 2016, pp. 61-84.
[http://dx.doi.org/10.1007/978-81-322-2647-5_4]
[38]
Cox, D.E.; Dyer, S.; Weir, R.; Cheseto, X.; Sturrock, M.; Coyne, D.; Torto, B.; Maule, A.G.; Dalzell, J.J. ABC transporter genes ABC-C6 and ABC-G33 alter plant-microbe-parasite interactions in the rhizosphere. Sci. Rep., 2019, 9(1), 19899.
[http://dx.doi.org/10.1038/s41598-019-56493-w] [PMID: 31882903]
[39]
Chandra, A.K.; Kumar, A.; Bharati, A.; Joshi, R.; Agrawal, A.; Kumar, S. Microbial-assisted and genomic-assisted breeding: a two way approach for the improvement of nutritional quality traits in agricultural crops. 3 Biotech, 2020, 10(2)
[40]
Bhattacharyya, C.; Bakshi, U.; Mallick, I.; Mukherji, S.; Bera, B.; Ghosh, A. Genome-guided insights into the plant growth promotion capabilities of the physiologically versatile Bacillus aryabhattai strain AB21. Front. Microbiol., 2017, 8, 411.
[http://dx.doi.org/10.3389/fmicb.2017.00411] [PMID: 28377746]
[41]
Matteoli, F.P.; Passarelli-Araujo, H.; Reis, R.J.A.; da Rocha, L.O.; de Souza, E.M.; Aravind, L.; Olivares, F.L.; Venancio, T.M. Genome sequencing and assessment of plant growth-promoting properties of a Serratia marcescens strain isolated from vermi compost. BMC Genomics, 2018, 19(1), 750.
[http://dx.doi.org/10.1186/s12864-018-5130-y] [PMID: 30326830]
[42]
Shariati, J.V.; Malboobi, M.A.; Tabrizi, Z.; Tavakol, E.; Owilia, P.; Safari, M. Comprehensive genomic analysis of a plant growth-promoting rhizobacterium Pantoea agglomerans strain P5. Sci. Rep., 2017, 7(1), 15610.
[http://dx.doi.org/10.1038/s41598-017-15820-9] [PMID: 29142289]
[43]
Zhang, L.N.; Wang, D.C.; Hu, Q.; Dai, X.Q.; Xie, Y.S.; Li, Q.; Liu, H.M.; Guo, J.H. Consortium of plant growth-promoting rhizobacteria strains suppresses sweet pepper disease by altering the rhizosphere microbiota. Front. Microbiol., 2019, 10, 1668.
[http://dx.doi.org/10.3389/fmicb.2019.01668] [PMID: 31396185]
[44]
Surico, G. The concepts of plant pathogenicity, virulence/avirulence and effector proteins by a teacher of plant pathology. Phytopathol. Mediterr., 2013, 52(3), 399-417.
[45]
Hammond-Kosack, K.E.; Jones, J.D.G. Plant disease resistance genes. Annu. Rev. Plant Physiol. Plant Mol. Biol., 1997, 48, 575-607.
[http://dx.doi.org/10.1146/annurev.arplant.48.1.575] [PMID: 15012275]
[46]
Doughari, J.H. An overview of plant immunity. Plant Pathol. Microbiol., 2015, 6, 322.
[47]
Flor, H.H. Host-parasite interaction in flax rust-its genetics and other implications. Phytopathology, 1955, 45, 680-685.
[48]
Jones, J.D.G.; Dangl, J.L. The plant immune system. Nature, 2006, 444(7117), 323-329.
[http://dx.doi.org/10.1038/nature05286] [PMID: 17108957]
[49]
Chinchilla, D.; Bauer, Z.; Regenass, M.; Boller, T.; Felix, G. The Arabidopsis receptor kinase FLS2 binds flg22 and determines the specificity of flagellin perception. Plant Cell, 2006, 18(2), 465-476.
[http://dx.doi.org/10.1105/tpc.105.036574] [PMID: 16377758]
[50]
Eckardt, N.A. Chitin signaling in plants: insights into the perception of fungal pathogens and rhizobacterial symbionts. Plant Cell, 2008, 20(2), 241-243.
[http://dx.doi.org/10.1105/tpc.108.058784] [PMID: 18285511]
[51]
Kunze, G.; Zipfel, C.; Robatzek, S.; Niehaus, K.; Boller, T.; Felix, G. The N terminus of bacterial elongation factor Tu elicits innate immunity in Arabidopsis plants. Plant Cell, 2004, 16(12), 3496-3507.
[http://dx.doi.org/10.1105/tpc.104.026765] [PMID: 15548740]
[52]
Brutus, A.; Sicilia, F.; Macone, A.; Cervone, F.; De Lorenzo, G. A domain swap approach reveals a role of the plant wall-associated kinase 1 (WAK1) as a receptor of oligo galacturonides. Proc. Natl. Acad. Sci. USA, 2010, 107(20), 9452-9457.
[http://dx.doi.org/10.1073/pnas.1000675107] [PMID: 20439716]
[53]
Choi, J.; Tanaka, K.; Cao, Y.; Qi, Y.; Qiu, J.; Liang, Y.; Lee, S.Y.; Stacey, G. Identification of a plant receptor for extracellular ATP. Science, 2014, 343(6168), 290-294.
[http://dx.doi.org/10.1126/science.343.6168.290] [PMID: 24436418]
[54]
Boller, T.; Felix, G. A renaissance of elicitors: perception of microbe-associated molecular patterns and danger signals by pattern-recognition receptors. Annu. Rev. Plant Biol., 2009, 60, 379-406.
[http://dx.doi.org/10.1146/annurev.arplant.57.032905.105346] [PMID: 19400727]
[55]
Hou, S.; Yang, Y.; Wu, D.; Zhang, C. Plant immunity: evolutionary insights from PBS1, Pto, and RIN4. Plant Signal. Behav., 2011, 6(6), 794-799.
[http://dx.doi.org/10.4161/psb.6.6.15143] [PMID: 21494098]
[56]
Puhar, A.; Sansonetti, P.J. Type III secretion system. Curr. Biol., 2014, 24(17), R784-R791.
[http://dx.doi.org/10.1016/j.cub.2014.07.016] [PMID: 25202865]
[57]
Balint-Kurti, P. The plant hypersensitive response: concepts, control and consequences. Mol. Plant Pathol., 2019, 20(8), 1163-1178.
[http://dx.doi.org/10.1111/mpp.12821] [PMID: 31305008]
[58]
Mandadi, K.K.; Scholthof, K.B. Plant immune responses against viruses: how does a virus cause disease? Plant Cell, 2013, 25(5), 1489-1505.
[http://dx.doi.org/10.1105/tpc.113.111658] [PMID: 23709626]
[59]
Cook, D.E.; Mesarich, C.H.; Thomma, B.P.H.J. Understanding plant immunity as a surveillance system to detect invasion. Annu. Rev. Phytopathol., 2015, 53(1), 541-563.
[http://dx.doi.org/10.1146/annurev-phyto-080614-120114] [PMID: 26047564]
[60]
van der Burgh, A.M.; Joosten, M.H.A.J. Plant immunity: thinking outside and inside the box. Trends Plant Sci., 2019, 24(7), 587-601.
[http://dx.doi.org/10.1016/j.tplants.2019.04.009] [PMID: 31171472]
[61]
Borrelli, V.M.G.; Brambilla, V.; Rogowsky, P.; Marocco, A.; Lanubile, A.M.G.; Brambilla, V.; Rogowsky, P.; Marocco, A.; Lanubile, A. The enhancement of plant disease resistance using CRISPR/Cas9 technology. Front. Plant Sci., 2018, 9, 1245.
[http://dx.doi.org/10.3389/fpls.2018.01245]] [PMID: 30197654]
[62]
Ahmad, S.; Wei, X.; Sheng, Z.; Hu, P.; Tang, S. CRISPR/Cas9 for development of disease resistance in plants: recent progress, limitations and future prospects. Brief. Funct. Genomics, 2020, 19(1), 26-39.
[http://dx.doi.org/10.1093/bfgp/elz041] [PMID: 31915817]
[63]
Oliva, R.; Ji, C.; Atienza-Grande, G.; Huguet-Tapia, J.C.; Perez-Quintero, A.; Li, T.; Eom, J.S.; Li, C.; Nguyen, H.; Liu, B.; Auguy, F.; Sciallano, C.; Luu, V.T.; Dossa, G.S.; Cunnac, S.; Schmidt, S.M.; Slamet-Loedin, I.H.; Vera Cruz, C.; Szurek, B.; Frommer, W.B.; White, F.F.; Yang, B. Broad-spectrum resistance to bacterial blight in rice using genome editing. Nat. Biotechnol., 2019, 37(11), 1344-1350.
[http://dx.doi.org/10.1038/s41587-019-0267-z] [PMID: 31659337]
[64]
Wang, T.; Zhang, H.; Zhu, H. CRISPR technology is revolutionizing the improvement of tomato and other fruit crops. Hortic. Res., 2019, 6, 77.
[http://dx.doi.org/10.1038/s41438-019-0159-x] [PMID: 31240102]
[65]
Muñoz, I.V.; Sarrocco, S.; Malfatti, L.; Baroncelli, R.; Vannacci, G. CRISPR-Cas for fungal genome editing: A new tool for the management of plant diseases. Front. Plant Sci., 2019, 10, 135.
[http://dx.doi.org/10.3389/fpls.2019.00135] [PMID: 30828340]
[66]
de Lamo, F.J.; Constantin, M.E.; Fresno, D.H.; Boeren, S.; Rep, M.; Takken, F.L.W. Xylem Sap Proteomics reveals distinct differences between R gene and endophyte-mediated resistance against Fusarium wilt disease in tomato. Front. Microbiol., 2018, 9, 2977.
[http://dx.doi.org/10.3389/fmicb.2018.02977] [PMID: 30564219]
[67]
Broberg, M.; Dubey, M.; Sun, M.H.; Ihrmark, K.; Schroers, H.J.; Li, S.D.; Jensen, D.F.; Brandström, D.M.; Karlsson, M. Out in the cold: identification of genomic regions associated with cold tolerance in the biocontrol fungus clonostachysrosea through genome-wide association mapping. Front. Microbiol., 2018, 9, 2844.
[http://dx.doi.org/10.3389/fmicb.2018.02844] [PMID: 30524411]
[68]
Bartoli, C.; Roux, F. Genome-wide association studies in plant pathosystems: toward an ecological genomics approach. Front. Plant Sci., 2017, 8, 763.
[http://dx.doi.org/10.3389/fpls.2017.00763] [PMID: 28588588]
[69]
Arora, S.; Steuernagel, B.; Gaurav, K.; Chandramohan, S.; Long, Y.; Matny, O.; Johnson, R.; Enk, J.; Periyannan, S.; Singh, N.; Asyraf, M.H.M.; Athiyannan, N.; Cheema, J.; Yu, G.; Kangara, N.; Ghosh, S.; Szabo, L.J.; Poland, J.; Bariana, H.; Jones, J.D.G.; Bentley, A.R.; Ayliffe, M.; Olson, E.; Xu, S.S.; Steffenson, B.J.; Lagudah, E.; Wulff, B.B.H. Resistance gene cloning from a wild crop relative by sequence capture and association genetics. Nat. Biotechnol., 2019, 37(2), 139-143.
[http://dx.doi.org/10.1038/s41587-018-0007-9] [PMID: 30718880]
[70]
Kim, S.M.; Reinke, R.F. A novel resistance gene for bacterial blight in rice, Xa43(t) identified by GWAS, confirmed by QTL mapping using a bi-parental population. PLoS One, 2019, 14(2)e0211775
[http://dx.doi.org/10.1371/journal.pone.0211775] [PMID: 30753229]
[71]
Xiao, Y.; Liu, H.; Wu, L.; Warburton, M.; Yan, J. Genome-wide association studies in maize: praise and stargaze. Mol. Plant, 2017, 10(3), 359-374.
[http://dx.doi.org/10.1016/j.molp.2016.12.008] [PMID: 28039028]
[72]
Raboin, L.M.; Ballini, E.; Tharreau, D.; Ramanantsoanirina, A.; Frouin, J.; Courtois, B.; Ahmadi, N. Association mapping of resistance to rice blast in upland field conditions. Rice (N. Y.), 2016, 9(1), 59.
[http://dx.doi.org/10.1186/s12284-016-0131-4] [PMID: 27830537]
[73]
Mgonja, E.M.; Balimponya, E.G.; Kang, H.; Bellizzi, M.; Park, C.H.; Li, Y.; Mabagala, R.; Sneller, C.; Correll, J.; Opiyo, S.; Talbot, N.J.; Mitchell, T.; Wang, G.L. Genome-wide association mapping of rice resistance genes against Magnaporthe oryzae isolates from four African countries. Phytopathology, 2016, 106(11), 1359-1365.
[http://dx.doi.org/10.1094/PHYTO-01-16-0028-R] [PMID: 27454702]
[74]
Karasov, T.L.; Kniskern, J.M.; Gao, L.; DeYoung, B.J.; Ding, J.; Dubiella, U.; Lastra, R.O.; Nallu, S.; Roux, F.; Innes, R.W.; Barrett, L.G.; Hudson, R.R.; Bergelson, J. The long-term maintenance of a resistance polymorphism through diffuse interactions. Nature, 2014, 512(7515), 436-440.
[http://dx.doi.org/10.1038/nature13439] [PMID: 25043057]
[75]
Roux, F.; Bergelson, J. The genetics underlying natural variation in the biotic interactions of Arabidopsis thaliana: the challenges of linking evolutionary genetics and community ecology. Curr. Top. Dev. Biol., 2016, 119, 111-156.
[http://dx.doi.org/10.1016/bs.ctdb.2016.03.001] [PMID: 27282025]
[76]
Lambrechts, L. Dissecting the genetic architecture of host-pathogen specificity. PLoS Pathog., 2010, 6(8) e1001019
[http://dx.doi.org/10.1371/journal.ppat.1001019] [PMID: 20700450]
[77]
Talas, F.; McDonald, B.A. Genome-wide analysis of Fusarium graminearum field populations reveals hotspots of recombination. BMC Genomics, 2015, 16, 996.
[http://dx.doi.org/10.1186/s12864-015-2166-0] [PMID: 26602546]
[78]
Dalman, K.; Himmelstrand, K.; Olson, Å.; Lind, M.; Brandström-Durling, M.; Stenlid, J. A genome-wide association study identifies genomic regions for virulence in the non-model organism Heterobasidion annosum s.s. PLoS One, 2013, 8(1) e53525
[http://dx.doi.org/10.1371/journal.pone.0053525] [PMID: 23341945]
[79]
Gao, Y.; Liu, Z.; Faris, J.D.; Richards, J.; Brueggeman, R.S.; Li, X.; Oliver, R.P.; McDonald, B.A.; Friesen, T.L. Validation of genome-wide association studies as a tool to identify virulence factors in Parastagonospora nodorum. Phytopathology, 2016, 106(10), 1177-1185.
[http://dx.doi.org/10.1094/PHYTO-02-16-0113-FI] [PMID: 27442533]
[80]
Wu, J.Q.; Sakthikumar, S.; Dong, C.; Zhang, P.; Cuomo, C.A.; Park, R.F. Comparative genomics integrated with association analysis identifies candidate effector genes corresponding to Lr20 in phenotype‐paired Puccinia triticina isolates from Australia. Front. Plant Sci., 2017, 8, 148.
[http://dx.doi.org/10.3389/fpls.2017.00148] [PMID: 28232843]
[81]
Wang, H.; Xu, X.; Vieira, F.G.; Xiao, Y.; Li, Z.; Wang, J.; Nielsen, R.; Chu, C. The power of inbreeding: NGS‐based GWAS of rice reveals convergent evolution during rice domestication. Mol. Plant, 2016, 9(7), 975-985.
[http://dx.doi.org/10.1016/j.molp.2016.04.018] [PMID: 27179918]
[82]
Morris, G.P.; Ramu, P.; Deshpande, S.P.; Hash, C.T.; Shah, T.; Upadhyaya, H.D.; Riera-Lizarazu, O.; Brown, P.J.; Acharya, C.B.; Mitchell, S.E.; Harriman, J.; Glaubitz, J.C.; Buckler, E.S.; Kresovich, S. Population genomic and genome-wide association studies of agro climatic traits in sorghum. Proc. Natl. Acad. Sci. USA, 2013, 110(2), 453-458.
[http://dx.doi.org/10.1073/pnas.1215985110] [PMID: 23267105]
[83]
Jia, G.; Huang, X.; Zhi, H.; Zhao, Y.; Zhao, Q.; Li, W.; Chai, Y.; Yang, L.; Liu, K.; Lu, H.; Zhu, C.; Lu, Y.; Zhou, C.; Fan, D.; Weng, Q.; Guo, Y.; Huang, T.; Zhang, L.; Lu, T.; Feng, Q.; Hao, H.; Liu, H.; Lu, P.; Zhang, N.; Li, Y.; Guo, E.; Wang, S.; Wang, S.; Liu, J.; Zhang, W.; Chen, G.; Zhang, B.; Li, W.; Wang, Y.; Li, H.; Zhao, B.; Li, J.; Diao, X.; Han, B. A haplotype map of genomic variations and genome-wide association studies of agronomic traits in foxtail millet (Setaria italica). Nat. Genet., 2013, 45(8), 957-961.
[http://dx.doi.org/10.1038/ng.2673] [PMID: 23793027]
[84]
Zhou, Z.; Jiang, Y.; Wang, Z.; Gou, Z.; Lyu, J.; Li, W.; Yu, Y.; Shu, L.; Zhao, Y.; Ma, Y.; Fang, C.; Shen, Y.; Liu, T.; Li, C.; Li, Q.; Wu, M.; Wang, M.; Wu, Y.; Dong, Y.; Wan, W.; Wang, X.; Ding, Z.; Gao, Y.; Xiang, H.; Zhu, B.; Lee, S.H.; Wang, W.; Tian, Z. Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean. Nat. Biotechnol., 2015, 33(4), 408-414.
[http://dx.doi.org/10.1038/nbt.3096] [PMID: 25643055]
[85]
Li, H.; Peng, Z.; Yang, X.; Wang, W.; Fu, J.; Wang, J.; Han, Y.; Chai, Y.; Guo, T.; Yang, N.; Liu, J.; Warburton, M.L.; Cheng, Y.; Hao, X.; Zhang, P.; Zhao, J.; Liu, Y.; Wang, G.; Li, J.; Yan, J. Genome-wide association study dissects the genetic architecture of oil biosynthesis in maize kernels. Nat. Genet., 2013, 45(1), 43-50.
[http://dx.doi.org/10.1038/ng.2484] [PMID: 23242369]
[86]
Wen, W.; Li, D.; Li, X.; Gao, Y.; Li, W.; Li, H.; Liu, J.; Liu, H.; Chen, W.; Luo, J.; Yan, J. Metabolome-based genome-wide association study of maize kernel leads to novel biochemical insights. Nat. Commun., 2014, 5, 3438.
[http://dx.doi.org/10.1038/ncomms4438] [PMID: 24633423]
[87]
Wang, X.; Pang, Y.; Zhang, J.; Wu, Z.; Chen, K.; Ali, J.; Ye, G.; Xu, J.; Li, Z. Genome-wide and gene-based association mapping for rice eating and cooking characteristics and protein content. Sci. Rep., 2017, 7(1), 17203.
[http://dx.doi.org/10.1038/s41598-017-17347-5] [PMID: 29222496]
[88]
Ramegowda, V.; Senthil-Kumar, M. The interactive effects of simultaneous biotic and abiotic stresses on plants: mechanistic understanding from drought and pathogen combination. J. Plant Physiol., 2015, 176, 47-54.
[http://dx.doi.org/10.1016/j.jplph.2014.11.008] [PMID: 25546584]
[89]
Tank, N.; Saraf, M. Salinity-resistant plant growth promoting rhizobacteria ameliorates sodium chloride stress on tomato plants. J. Plant Interact., 2010, 5(1), 51-58.
[http://dx.doi.org/10.1080/17429140903125848]
[90]
Fahad, S.; Hussain, S.; Bano, A.; Saud, S.; Hassan, S.; Shan, D.; Khan, F.A.; Khan, F.; Chen, Y.; Wu, C.; Tabassum, M.A.; Chun, M.X.; Afzal, M.; Jan, A.; Jan, M.T.; Huang, J. Potential role of phytohormones and plant growth-promoting rhizobacteria in abiotic stresses: consequences for changing environment. Environ. Sci. Pollut. Res. Int., 2015, 22(7), 4907-4921.
[http://dx.doi.org/10.1007/s11356-014-3754-2] [PMID: 25369916]
[91]
Penyalver, R.; Oger, P.; López, M.M.; Farrand, S.K. Iron-binding compounds from Agrobacterium spp.: biological control strain Agrobacterium rhizogenes K84 produces a hydroxamate siderophore. Appl. Environ. Microbiol., 2001, 67(2), 654-664.
[http://dx.doi.org/10.1128/AEM.67.2.654-664.2001] [PMID: 11157228]
[92]
Foolad, M.R. Genome mapping and molecular breeding of tomato. Int. J. Plant Genomics, 2007, 2007, 64358.
[http://dx.doi.org/10.1155/2007/64358] [PMID: 18364989]
[93]
Gupta, A.; Gopal, M.; Thomas, G.V.; Manikandan, V.; Gajewski, J.; Thomas, G.; Seshagiri, S.; Schuster, S.C.; Rajesh, P.; Gupta, R. Whole genome sequencing and analysis of plant growth promoting bacteria isolated from the rhizosphere of plantation crops coconut, cocoa and arecanut. PLoS One, 2014, 9(8) e104259
[http://dx.doi.org/10.1371/journal.pone.0104259] [PMID: 25162593]
[94]
Kumar, V.; Baweja, M.; Singh, P.K.; Shukla, P. Recent developments in systems biology and metabolic engineering of plant microbe interactions. Front. Plant Sci., 2016, 7, 1421.
[http://dx.doi.org/10.3389/fpls.2016.01421] [PMID: 27725824]
[95]
Kumar, A.; Verma, J.P. Does plant-Microbe interaction confer stress tolerance in plants: A review? Microbiol. Res., 2018, 207, 41-52.
[http://dx.doi.org/10.1016/j.micres.2017.11.004] [PMID: 29458867]
[96]
Grover, M.; Ali, S.Z.; Sandhya, V.; Rasul, A.; Venkateswarlu, B. Role of microorganisms in adaptation of agriculture crops to abiotic stresses. World J. Microbiol. Biotechnol., 2010, 27(5), 1231-1240.
[http://dx.doi.org/10.1007/s11274-010-0572-7]
[97]
Cohen, A.C.; Bottini, R.; Pontin, M.; Berli, F.J.; Moreno, D.; Boccanlandro, H.; Travaglia, C.N.; Piccoli, P.N. Azospirillum brasilense ameliorates the response of Arabidopsis thaliana to drought mainly via enhancement of ABA levels. Physiol. Plant., 2015, 153(1), 79-90.
[http://dx.doi.org/10.1111/ppl.12221] [PMID: 24796562]
[98]
Choudhary, D.K.; Kasotia, A.; Jain, S.; Vaishnav, A.; Kumari, S.; Sharma, K.P.; Varma, A. Bacterial-mediated tolerance and resistance to plants under abiotic and biotic stresses. J. Plant Growth Regul., 2015, 35, 276-300.
[http://dx.doi.org/10.1007/s00344-015-9521-x]
[99]
Savci, S. An agricultural pollutant: chemical fertiliser. Int. J. Environ. Sci. Technol., 2012, 3, 77-80.
[100]
Naik, K.; Mishra, S.; Srichandan, H.; Singh, P.K.; Sarangi, P.K. Plant growth promoting microbes: Potential link to sustainable agriculture and environment. Biocatal. Agric. Biotechnol., 2019, 21101356
[101]
Parnell, J.J.; Berka, R.; Young, H.A.; Sturino, J.M.; Kang, Y.; Barnhart, D.M.; DiLeo, M.V. andDiLeo, M.V. From the lab to the farm: an industrial perspective of plant beneficial microorganisms. Front. Plant Sci., 2016, 7, 1110.
[http://dx.doi.org/10.3389/fpls.2016.01110] [PMID: 27540383]
[102]
Nathiya, S.; Janani, R.; Kannan, V.R. Potential of plant growth promoting rhizobacteria to overcome the exposure of pesticide in Trigonellafoenum–graecum (fenugreek leaves). Biocatal. Agric. Biotechnol., 2020, 140, 101493
[http://dx.doi.org/10.1016/j.bcab.2020.101493]]
[103]
Puri, A.; Padda, K.P.; Chanway, C.P. Can naturally-occurring endophytic nitrogen-fixing bacteria of hybrid white spruce sustain boreal forest tree growth on extremely nutrient-poor soils? Soil Biol. Biochem., 2020, 140 107642
[http://dx.doi.org/10.1016/j.soilbio.2019.107642]
[104]
Cunningham, J.E.; Kuiack, C. Production of citric and oxalic acids and solubilization of calcium phosphate by Penicillium bilaii. Appl. Environ. Microbiol., 1992, 58(5), 1451-1458.
[http://dx.doi.org/10.1128/AEM.58.5.1451-1458.1992] [PMID: 1622211]
[105]
Ferreira, L.D.V.S.M.; Carvalho, F.D.; Andrade, J.F.C.; Oliveira, D.P.; Medeiros, F.H.V.D.; Moreira, F.M.D.S. Co-inoculation of selected nodule endophytic rhizobacterial strains with Rhizobium tropici promotes plant growth and controls damping off in common bean. Pedosphere, 2020, 30(1), 98-108.
[http://dx.doi.org/10.1016/S1002-0160(19)60825-8]
[106]
Azabou, M.C.; Gharbi, Y.; Medhioub, I. Ennouri, K.; Barham, H.; Tounsi, S.; Triki, M. A. The endophytic strain Bacillus velezensis OEE1: An efficient biocontrol agent against Verticillium wilt of olive and a potential plant growth promoting bacteria. Biol. Control, 2020, 143 104168
[http://dx.doi.org/10.1016/j.biocontrol.2019.104168]
[107]
Müller, C.A.; Obermeier, M.M.; Berg, G. Bioprospecting plant-associated microbiomes. J. Biotechnol., 2016, 235, 171-180.
[http://dx.doi.org/10.1016/j.jbiotec.2016.03.033] [PMID: 27015976]
[108]
Zachow, C.; Müller, H.; Tilcher, R.; Donat, C.; Berg, G. Catch the best: novel screening strategy to select stress protecting agents for crop plants. Agronomy (Basel), 2013, 3, 794-815.
[http://dx.doi.org/10.3390/agronomy3040794]
[109]
Delmotte, N.; Knief, C.; Chaffron, S.; Innerebner, G.; Roschitzki, B.; Schlapbach, R.; von Mering, C.; Vorholt, J.A. Community proteogenomics reveals insights into the physiology of phyllosphere bacteria. Proc. Natl. Acad. Sci. USA, 2009, 106(38), 16428-16433.
[http://dx.doi.org/10.1073/pnas.0905240106] [PMID: 19805315]
[110]
Knief, C.; Delmotte, N.; Chaffron, S.; Stark, M.; Innerebner, G.; Wassmann, R.; von Mering, C.; Vorholt, J.A. Metaproteogenomic analysis of microbial communities in the phyllosphere and rhizosphere of rice. ISME J., 2012, 6(7), 1378-1390.
[http://dx.doi.org/10.1038/ismej.2011.192] [PMID: 22189496]
[111]
Mendes, L.W.; Kuramae, E.E.; Navarrete, A.A.; van Veen, J.A.; Tsai, S.M. Taxonomical and functional microbial community selection in soybean rhizosphere. ISME J., 2014, 8(8), 1577-1587.
[http://dx.doi.org/10.1038/ismej.2014.17] [PMID: 24553468]
[112]
Tikariha, H.; Purohit, H.J. Assembling a genome for novel nitrogen-fixing bacteria with capabilities for utilization of aromatic hydrocarbons. Genomics, 2019, 111(6), 1824-1830.
[http://dx.doi.org/10.1016/j.ygeno.2018.12.005] [PMID: 30552976]
[113]
Hao, D.C.; Xiao, P. Rhizosphere microbiota and microbiome of medicinal plants: from molecular biology to omics approaches. Chin. Herb. Med., 2017, 9(3), 199-217.
[http://dx.doi.org/10.1016/S1674-6384(17)60097-2]
[114]
Sarhan, M.S.; Hamza, M.A.; Youssef, H.H.; Patz, S.; Becker, M.; ElSawey, H.; Nemr, R.; Daanaa, H.A.; Mourad, E.F.; Morsi, A.T.; Abdelfadeel, M.R.; Abbas, M.T.; Fayez, M.; Ruppel, S.; Hegazi, N.A. Culturomics of the plant prokaryotic microbiome and the dawn of plant-based culture media - a review. J. Adv. Res., 2019, 19, 15-27.
[http://dx.doi.org/10.1016/j.jare.2019.04.002] [PMID: 31341666]
[115]
Knief, C. Analysis of plant microbe interactions in the era of next generation sequencing technologies. Front. Plant Sci., 2014, 5, 216.
[http://dx.doi.org/10.3389/fpls.2014.00216] [PMID: 24904612]
[116]
Kankanala, P.; Nandety, R.S.; Mysore, K.S. Genomics of plant disease resistance in legumes. Front. Plant Sci., 2019, 10, 1345.
[http://dx.doi.org/10.3389/fpls.2019.01345] [PMID: 31749817]

Rights & Permissions Print Cite
© 2024 Bentham Science Publishers | Privacy Policy