Abstract
Most agronomically important traits, including resistance against pathogens, are governed by quantitative trait loci (QTL). QTL-mediated resistance shows promise of being effective and long-lasting against diverse pathogens. Identification of genes controlling QTL-based disease resistance contributes to breeding for cultivars that exhibit high and stable resistance. Several defense response genes have been successfully used as good predictors and contributors to QTL-based resistance against several devastating rice diseases. In this study, we identified and characterized a rice (Oryza sativa) mutant line containing a 750 bp deletion in the second exon of OsPAL4, a member of the phenylalanine ammonia-lyase gene family. OsPAL4 clusters with three additional OsPAL genes that co-localize with QTL for bacterial blight and sheath blight disease resistance on rice chromosome 2. Self-pollination of heterozygous ospal4 mutant lines produced no homozygous progeny, suggesting that homozygosity for the mutation is lethal. The heterozygous ospal4 mutant line exhibited increased susceptibility to three distinct rice diseases, bacterial blight, sheath blight, and rice blast. Mutation of OsPAL4 increased expression of the OsPAL2 gene and decreased the expression of the unlinked OsPAL6 gene. OsPAL2 function is not redundant because the changes in expression did not compensate for loss of disease resistance. OsPAL6 co-localizes with a QTL for rice blast resistance, and is down-regulated in the ospal4 mutant line; this may explain enhanced susceptibility to Magnoporthe oryzae. Overall, these results suggest that OsPAL4 and possibly OsPAL6 are key contributors to resistance governed by QTL and are potential breeding targets for improved broad-spectrum disease resistance in rice.
Similar content being viewed by others
References
Achnine L, Blancaflor EB, Rasmussen S et al (2004) Colocalization of l-phenylalanine ammonia-lyase and cinnamate 4-hydroxylase for metabolic channeling in phenylpropanoid biosynthesis. Plant Cell 16:3098–3109. doi:10.1105/tpc.104.024406
Bagali PG, Hittalmani S, Srinivasachary KS et al (1998) Genetic markers associated with field resistance to leaf and neck blast across locations in rice (Oryza sativa L.). Rice Genet Newsl 15:128–131
Ballini E, Morel J-B, Droc G et al (2008) A genome-wide meta-analysis of rice blast resistance genes and quantitative trait loci provides new insights into partial and complete resistance. Mol Plant Microbe Interact 21:859–868. doi:10.1094/MPMI-21-7-0859
Bate NJ, Orr J, Ni W et al (1994) Quantitative relationship between phenylalanine ammonia-lyase levels and phenylpropanoid accumulation in transgenic tobacco identifies a rate-determining step in natural product synthesis. Proc Natl Acad Sci USA 91:7608–7612
Becker-Andre M, Schulze-Lefert P, Hahlbrock K (1991) Structural comparison, modes of expression, and putative cis-acting elements of the two 4-coumarate:CoA ligase genes in potato. J Biol Chem 266:8551–8559
Beckers GJM, Spoel SH (2006) Fine-tuning plant defence signalling: salicylate versus jasmonate. Plant Biol (Stuttg) 8:1–10. doi:10.1055/s-2005-872705
Bhat WW, Razdan S, Rana S et al (2014) A phenylalanine ammonia-lyase ortholog (PkPAL1) from Picrorhiza kurrooa Royle ex. Benth: molecular cloning, promoter analysis and response to biotic and abiotic elicitors. Gene 547:245–256. doi:10.1016/j.gene.2014.06.046
Boerjan W, Ralph J, Baucher M (2003) Lignin biosynthesis. Annu Rev Plant Biol 54:519–546. doi:10.1146/annurev.arplant.54.031902.134938
Bowles DJ (1990) Defense-related proteins in higher plants. Annu Rev Biochem 59:873–907
Boyd L, Ridout C, O’Sullivan DM et al (2013) Plant-pathogen interactions: disease resistance in modern agriculture. Trends Genet 29:233–240. doi:10.1016/j.tig.2012.10.011
Calabrese JC, Jordan DB, Boodhoo A et al (2004) Crystal structure of phenylalanine ammonia lyase: multiple helix dipoles implicated in catalysis. Biochemistry 43:11403–11416. doi:10.1021/bi049053
Chen F, Dixon R (2007) Lignin modification improves fermentable sugar yields for biofuel production. Nat Biotechnol 25:759–761. doi:10.1038/nbt1316
Chen F, Srinivasa Reddy MS, Temple S et al (2006) Multi-site genetic modulation of monolignol biosynthesis suggests new routes for formation of syringyl lignin and wall-bound ferulic acid in alfalfa (Medicago sativa L.). Plant J 48:113–124. doi:10.1111/j.1365-313X.2006.02857.x
Chen L-N, Yang Y, Yan C-Q et al (2012) Identification of quantitative trait loci for bacterial blight resistance derived from Oryza meyeriana and agronomic traits in recombinant inbred lines of Oryza sativa. J Phytopathol 160:461–468. doi:10.1111/j.1439-0434.2012.01931.x
Chisholm ST, Coaker G, Day B, Staskawicz BJ (2006) Host-microbe interactions: shaping the evolution of the plant immune response. Cell 124:803–814. doi:10.1016/j.cell.2006.02.008
Coquoz J, Buchala A, Metraux J (1998) The biosynthesis of salicylic acid in potato plants. Plant Physiol 117:1095–1101
Cramer CL, Ryder TB, Bell JN et al (1985) Rapid switching of plant gene-expression induced by fungal elicitor. Science 80(227):1240–1243. doi:10.1126/science.227.4691.1240
Craven-Bartle B, Pascual MB, Cánovas FM, Avila C (2013) A Myb transcription factor regulates genes of the phenylalanine pathway in maritime pine. Plant J 74:755–766. doi:10.1111/tpj.12158
Cui Y, Magill J, Frederiksen R, Magill C (1996) Chalcone synthase and phenylalanine ammonia-lyase mRNA levels following exposure of sorghum seedlings to three fungal pathogens. Physiol Mol Plant Pathol 49:187–199. doi:10.1006/pmpp.1996.0048
Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution (N Y) 39:783–791
Fu D, Chen L, Yu G et al (2011) QTL mapping of sheath blight resistance in a deep-water rice cultivar. Euphytica 180:209–218. doi:10.1007/s10681-011-0366-5
Fukuoka S, Okuno K (2001) QTL analysis and mapping of pi21, a recessive gene for field resistance to rice blast in Japanese upland rice. Theor Appl Genet 103:185–190. doi:10.1007/s001220100611
Gassmann W, Bhattacharjee S (2012) Effector-triggered immunity signaling: from gene-for-gene pathways to protein-protein interaction networks. Mol Plant Microbe Interact 25:862–868
Giberti S, Bertea CM, Narayana R et al (2012) Two phenylalanine ammonia lyase isoforms are involved in the elicitor-induced response of rice to the fungal pathogen Magnaporthe oryzae. J Plant Physiol 169:249–254. doi:10.1016/j.jplph.2011.10.008
Gruner K, Griebel T, Návarová H et al (2013) Reprogramming of plants during systemic acquired resistance. Front Plant Sci 4:1–28. doi:10.3389/fpls.2013.00252
Gupta SK, Rai AK, Kanwar SS et al (2012) The single functional blast resistance gene Pi54 activates a complex defence mechanism in rice. J Exp Bot 63:757–772. doi:10.1093/jxb/err297
Hahlbrock K, Scheel D (1989) Physiology and molecular biology of phenylpropanoid metabolism. Annu Rev Plant Physiol Plant Mol Biol 40:347–369
Havir EA, Hanson KR (1973) L-phenylalanine ammonia-lyase (maize and potato). Evidence that the enzyme is composed of four subunits. Biochemistry 12:1583–1591
Huang J, Zhao X, Cheng K, Jiang Y, Ouyang Y, Xu C, Li X, Xiao J, Zhang Q (2013) OsAP65, a rice aspartic protease, is essential for male fertility and plays a role in pollen germination and pollen tube growth. J Exp Bot 64:3351–3360
Jain M, Nijhawan A, Tyagi AK, Khurana JP (2006) Validation of housekeeping genes as internal control for studying gene expression in rice by quantitative real-time PCR. Biochem Biophys Res Commun 345:646–651. doi:10.1016/j.bbrc.2006.04.140
Jia Y, Valent B, Lee FN (2003) Determination of host responses to Magnaporthe grisea on detached rice leaves. Plant Dis 87:129–133
Jia Y, Liu G, Park D, Yang Y (2013) Inoculation and scoring methods for rice sheath blight disease. In: Yang Y (ed) Rice Protoc. Humana Press, Totowa, NJ, pp 257–268
Jones JDG, Dangl JL (2006) The plant immune system. Nature 444:323–329. doi:10.1038/nature05286
Joos HJ, Hahlbrock K (1992) Phenylalanine ammonia-lyase in potato (Solanum tuberosum L): genomic complexity, structural comparison of 2 selected genes and modes of expression. Eur J Biochem 204:621–629
Kauffman HE, Reddy APK, Hsiek SPV, Marca SD (1973) An improved technique for evaluating resistance of race varieties to Xanthomonas oryzae. Plant Dis Rep 57:537–541
Kim DS, Hwang BK (2014) An important role of the pepper phenylalanine ammonia-lyase gene (PAL1) in salicylic acid-dependent signalling of the defence response to microbial pathogens. J Exp Bot 65:2295–2306. doi:10.1093/jxb/eru109
Kim Y, Tsuda K, Igarashi D et al (2014) Signaling mechanisms underlying the robustness and tunability of the plant immune network. Cell Host Microbe 15:84–94. doi:10.1016/j.chom.2013.12.002
Kou Y, Wang S (2010) Broad-spectrum and durability: understanding of quantitative disease resistance. Curr Opin Plant Biol 13:181–185. doi:10.1016/j.pbi.2009.12.010
La Camera S, Gouzerh G, Dhondt S et al (2004) Metabolic reprogramming in plant innate immunity : the contributions of phenylpropanoid and oxylipin pathways. Immunol Rev 198:267–284
Lee H, Leon J, Raskin I (1995) Biosynthesis and metabolism of salicylic acid. Proc Natl Acad Sci USA 92:4076–4079
Li ZK, Luo LJ, Mei HW et al (1999) A “defeated” rice resistance gene acts as a QTL against a virulent strain of Xanthomonas oryzae pv. oryzae. Mol Gen Genet 261:58–63
Li B, Liu B, Shan C et al (2013) Antibacterial activity of two chitosan solutions and their effect on rice bacterial leaf blight and leaf streak. Pest Manag Sci 69:312–320. doi:10.1002/ps.3399
Liao Y, Li H, Kreuzaler F, Fischer R (1996) Nucleotide sequence of one of two tandem genes (Accesion No.X99705) encoding phenylalanine ammonia-lyase in Triticum aestivum. Plant Physiol 112:1398
Liu B, Zhang S, Zhu X et al (2004) Candidate defense genes as predictors of quantitative blast resistance in rice. Mol Plant Microbe Interact 17:1146–1152. doi:10.1094/MPMI.2004.17.10.1146
Logemann E, Parniske M, Hahlbrock K (1995) Modes of expression and common structural features of the complete phenylalanine ammonia-lyase gene family in parsley. Proc Natl Acad Sci USA 92:5905–5909. doi:10.1073/pnas.92.13.5905
Maher E, Bate NJ, Ni W et al (1994) Increased disease susceptibility of transgenic tobacco plants with suppressed levels of preformed phenylpropanoid products. Proc Natl Acad Sci USA 91:7802–7806
Malamy J, Carr JP, Klessig DF, Raskin I (2014) Salicylic acid : a likely endogenous signal in the resistance response of tobacco to viral infection. Science 80(250):1002–1004
Manosalva PM, Davidson RM, Liu B et al (2009) A germin-like protein gene family functions as a complex quantitative trait locus conferring broad-spectrum disease resistance in rice. Plant Physiol 149:286–296. doi:10.1104/pp.108.128348
Mauch-Mani B, Slusarenko J (1996) Production of salicylic acid precursors is a major function of phenylalanine ammonia-lyase in the resistance of Arabidopsis to Peronospora parasitica. Plant Cell 8:203–212. doi:10.1105/tpc.8.2.203
Moffitt MC, Louie GV, Bowman ME et al (2007) Discovery of two cyanobacterial phenylalanine ammonia lyases: kinetic and structural characterization. Biochemistry 46:1004–1012
Naoumkina MA, Zhao Q, Gallego-giraldo L et al (2010) Genome-wide analysis of phenylpropanoid defence pathways. Mol Plant Pathol 11:829–846. doi:10.1111/J.1364-3703.2010.00648.X
Ouyang S, Zhu W, Hamilton J et al (2007) The TIGR rice genome annotation resource: improvements and new features. Nucleic Acids Res 35:D883–D887. doi:10.1093/nar/gkl976
Pallas JA, Paiva NL, Lamb C, Dixon RA (1996) Tobacco plants epigenetically suppressed in phenylalanine ammonia-lyase expression do not develop systemic acquired resistance in response to infection by tobacco mosaic virus. Plant J 10:281–293
Pfaffl MW (2001) A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res 29:2002–2007
Pinson SRM, Capdevielle FM, Oard JH (2005) Confirming QTLs and finding additional loci conditioning sheath blight resistance in rice using recombinant inbred lines. Crop Sci 45:503–510
Ramalingam J, Vera Cruz CM, Kukreja K et al (2003) Candidate defense genes from rice, barley, and maize and their association with qualitative and quantitative resistance in rice. Mol Plant Microbe Interact 16:14–24. doi:10.1094/MPMI.2003.16.1.14
Rawal HC, Singh NK, Sharma TR (2013) Conservation, divergence, and genome-wide distribution of PAL and POX A gene families in plants. Int J Genomics 2013:1–10. doi:10.1155/2013/678969
Reichert AI, He X-Z, Dixon R (2009) Phenylalanine ammonia-lyase (PAL) from tobacco (Nicotiana tabacum): characterization of the four tobacco PAL genes and active heterotetrameric enzymes. Biochem J 424:233–242. doi:10.1042/BJ20090620
Reimers P, Leach JE (1991) Race-specific resistance to Xanthomonas oryzae pv. oryzae conferred by bacterial blight resistance gene Xa-10 in rice (Oryza sativa) involves accumulation of a lignin-like substance in host tissues. Physiol Mol Plant Pathol 38:39–55
Rensing S (2014) Gene duplication as a driver of plant morphogenetic evolution. Curr Opin Plant Biol 17:43–48. doi:10.1016/j.pbi.2013.11.002
Riaz A, Riaz A, Rattu AUR et al (2014) Phenylalanine ammonia-lyase (PAL) and peroxidase activity in brown rust infected tissues of Pakistani wheat cultivars. Pak J Bot 46:1101–1107
Ride JP (1983) Cell walls and other structural barriers in defence. Biochem Plant Pathol (Callow, JA, ed) pp 215–236
Ritter H, Schulz GE (2004) Structural basis for the entrance into the phenylpropanoid metabolism catalyzed by phenylalanine ammonia-lyase. Plant Cell 16:3426–3436
Rohde A, Morreel K, Ralph J et al (2004) Molecular phenotyping of the pal1 and pal2 mutants of Arabidopsis thaliana reveals far-reaching consequences on phenylpropanoid, amino acid, and carbohydrate metabolism. Plant Cell 16:2749–2771. doi:10.1105/tpc.104.023705.phospho
Saghai-Maroof M, Soliman KM, Jorgensen R, Allard RW (1984) Ribosomal DNA spacer-length polymorphisms in barley: mendelian inheritance, chromosomal location, and population dynamics. Proc Natl Acad Sci USA 81:8014–8018
Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425
Sana TR, Fischer S, Wohlgemuth G, Fiehn O (2010) Metabolomic and transcriptomic analysis of the rice response to the bacterial blight pathogen Xanthomonas oryzae pv. oryzae. Metabolomics 6:451–465. doi:10.1007/s11306-010-0218-7
Sarma AD, Sharma R (1999) Purification and characterization of UV-B induced phenylalanine ammonia-lyase from rice seedlings. Phytochemistry 50:729–737
Savary S, Mila A, Willocquet L et al (2011) Risk factors for crop health under global change and agricultural shifts: a framework of analyses using rice in tropical and subtropical Asia as a model. Phytopathology 101:696–709. doi:10.1094/PHYTO-07-10-0183
Schatz MC, Maron LG, Stein JC, et al (2014) New whole genome de novo assemblies of three divergent strains of rice (O. sativa) documents novel gene space of aus and indica. BioRxiv http://biorxiv.org
Schuler GD (1997) Sequence mapping by electronic PCR. Genome Res 7:541–550
Shang Q-M, Li L, Dong C-J (2012) Multiple tandem duplication of the phenylalanine ammonia-lyase genes in Cucumis sativus L. Planta 236:1093–1105. doi:10.1007/s00425-012-1659-1
Shiraishi T, Yamada T, Nicholson RL, Kunoh H (1995) Phenylalanine ammonia-lyase in barley: activity enhancement in response to Erysiphe graminis f.sp. hordei (race 1) a pathogen, and Erysiphe-pisi, a nonpathogen. Physiol Mol Plant Pathol 46:153–162. doi:10.1006/pmpp.1995.1012
Sommssich IE, Hahlbrock K (1998) Pathogen defence in plants: a paradigm of biological complexity. Trends Plant Sci 3:86–90
Stern DL (2013) The genetic causes of convergent evolution. Nat Rev Genet 14:751–764. doi:10.1038/nrg3483
Tamura K, Stecher G, Peterson D et al (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729. doi:10.1093/molbev/mst197
Tanaka N, Che F-S, Watanabe N et al (2003) Flagellin from an incompatible strain of Acidovorax avenae mediates H2O2 generation accompanying hypersensitive cell death and expression of PAL, Cht-1, and PBZ1, but not of Lox in rice. Mol Plant Microbe Interact 16:422–428. doi:10.1094/MPMI.2003.16.5.422
Tanger P, Field JL, Jahn CE et al (2013) Biomass for thermochemical conversion: targets and challenges. Front Plant Sci 4:218. doi:10.3389/fpls.2013.00218
Trapnell C, Williams BA, Pertea G et al (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 28:511–515. doi:10.1038/nbt.1621
Trognitz F, Manosalva P, Gysin R et al (2002) Plant defense genes associated with quantitative resistance to potato late blight in Solanum phureja x dihaploid S. tuberosum hybrids. Mol Plant Microbe Interact 15:587–597. doi:10.1094/MPMI.2002.15.6.587
Vanholme R, Storme V, Vanholme B et al (2012) A systems biology view of responses to lignin biosynthesis perturbations in Arabidopsis. Plant Cell 24:3506–3529. doi:10.1105/tpc.112.102574
Venere RJ (1980) Role of peroxidase in cotton resistant to bacterial blight. Plant Sci Lett 20:47–56
Venu RC, Yulin J, Gowda M et al (2007) RL-SAGE and microarray analysis of the rice transcriptome after Rhizoctonia solani infection. Mol Genet Genomics 278:421–431. doi:10.1007/s00438-007-0260-y
Vogt T (2010) Phenylpropanoid biosynthesis. Mol Plant 3:2–20. doi:10.1093/mp/ssp106
Wamishe YA, Yulin J, Singh P, Cartwright RD (2007) Identification of field isolates of Rhizoctonia solani to detect quantitative resistance in rice under greenhouse conditions. Front Agric China 1:361–367. doi:10.1007/s11703-007-0061-4
Wang GL, Mackill DJ, Bonman JM et al (1994) RFLP mapping of genes conferring complete and partial resistance to blast in a durably resistant rice cultivar. Genetics 136:1421–1434
Wang Z, Taramino G, Yang D et al (2001) Rice ESTs with disease-resistance gene- or defense-response gene-like sequences mapped to regions containing major resistance genes or QTLs. Mol Genet Genomics 265:302–310. doi:10.1007/s004380000415
Wu JL, Sinha PK, Variar M et al (2004) Association between molecular markers and blast resistance in an advanced backcross population of rice. Theor Appl Genet 108:1024–1032
Wu J-L, Wu C, Lei C et al (2005) Chemical- and irradiation-induced mutants of indica rice IR64 for forward and reverse genetics. Plant Mol Biol 59:85–97. doi:10.1007/s11103-004-5112-0
Zhang G, Cui Y, Ding X, Dai Q (2013) Stimulation of phenolic metabolism by silicon contributes to rice resistance to sheath blight. J Plant Nutr Soil Sci 176:118—124. doi:10.1002/jpln.201200008
Zhou Y-L, Xie X-W, Xu M-R et al (2012) Genetic overlap in the quantitative resistance of rice at the seedling and adult stages to Xanthomonas oryzae pv. oryzae. J Plant Biol 55:102–113
Zhu Q, Dabi T, Beeche A et al (1995) Cloning and properties of a rice gene encoding phenylalanine ammonia-lyase. Plant Mol Biol 29:535–550
Zhu M, Wang L, Pan Q (2004) Identification and characterization of a new blast resistance gene located on rice chromosome 1 through linkage and differential analyses. Phytopathology 94:515–519. doi:10.1094/PHYTO.2004.94.5.515
Zuckerlandl E, Pauling L (1965) Evolutionary divergence and convergence in proteins. In: Bryson V, Vogel HJ (eds) Evolving genes and proteins. Academic Press, New York, pp 97–166
Acknowledgments
This research was supported by the Office of Biological and Environmental Research of the U.S. Department of Energy (DOE-BER, contract No. DE-FG02-08ER64629), an International Rice Research Institute (IRRI) and U.S. Agency for International Development (USAID) Linkage grant (DRPC2011-42), a USDA-CSREES-NRI-Rice-CAP grant 2004-35317-14867, and a National Institute of Food and Agriculture (USDA-NIFA) 2008-35504-0485. Tonnessen was supported by a fellowship from the CSU Program in Molecular Plant Biology, and Leach was supported by the Colorado State Experiment Station.
Conflict of interest
The authors declare that they have no conflict of interest.
Author information
Authors and Affiliations
Corresponding author
Additional information
Bradley W. Tonnessen and Patricia Manosalva have contributed equally to this work.
Electronic supplementary material
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Tonnessen, B.W., Manosalva, P., Lang, J.M. et al. Rice phenylalanine ammonia-lyase gene OsPAL4 is associated with broad spectrum disease resistance. Plant Mol Biol 87, 273–286 (2015). https://doi.org/10.1007/s11103-014-0275-9
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s11103-014-0275-9