Abstract
Fusarium yellows caused by Fusarium oxysporum f. sp. conglutinans is an important disease of Brassica worldwide. To identify a resistance (R) gene against Fusarium yellows in Chinese cabbage (Brassica rapa var. pekinensis), we analyzed differential expression at the whole genome level between resistant and susceptible inbred lines using RNA sequencing. Four hundred and eighteen genes were significantly differentially expressed, and these were enriched for genes involved in response to stress or stimulus. Seven dominant DNA markers at putative R-genes were identified. Presence and absence of the sequence of the putative R-genes, Bra012688 and Bra012689, correlated with the resistance of six inbred lines and susceptibility of four inbred lines, respectively. In F2 populations derived from crosses between resistant and susceptible inbred lines, presence of Bra012688 and Bra012689 cosegregated with resistance, suggesting that Bra012688 and Bra012689 are good candidates for fusarium yellows resistance in Chinese cabbage.
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References
Abe H, Narusaka Y, Sasaki I, Hatakeyama K, Shin-I S, Narusaka M, Fukami-Kobayashi K, Matsumoto S, Kobayashi M (2011) Development of full-length cDNAs from Chinese cabbage (Brassica rapa subsp. pekinensis) and identification of marker genes for defence response. DNA Res 18:277–289
Abe A, Kosugi S, Yoshida K, Natsume S, Takagi H, Kanzaki H, Matsumura H, Yoshida K, Mitsuoka C, Tamiru M, Innan H, Cano L, Kamoun S, Terauchi R (2012) Genome sequencing reveals agronomically important loci in rice using MutMap. Nat Biotechnol 30:174–178
Ashikawa I, Hayashi N, Yamane H, Kanamori H, Wu J, Matsumoto T, Ono K, Yano M (2008) Two adjacent nucleotide-binding site-leucine-rich repeat class genes are required to confer Pikm-specific rice blast resistance. Genetics 180:2267–2276
Austin RS, Vidaurre D, Stamatiou G, Breit R, Provart NJ, Bonetta D, Zhang J, Fung P, Gong Y, Wang PW, McCourt P, Guttman DS (2011) Next-generation map** of Arabidopsis genes. Plant J 67:715–725
Berrocal-Lobo M, Molina A (2008) Arabidopsis defense response against Fusarium oxysporum. Trends Plant Sci 13:145–150
Brotman Y, Normantovich M, Goldenberg Z, Zvirin Z, Kovalski I, Stovbun N, Doniger T, Bolger AM, Troadec C, Bendahmane A, Cohen R, Katzir N, Pitrat M, Dogimont C, Perl-Treves R (2013) Dual resistance of melon to Fusarium oxysporum races 0 and 2 and to Papaya ring-spot virus is controlled by a pair of head-to-head-oriented NB-LRR genes of unusual architecture. Mol Plant 6:235–238
Cacas JL, Petitot AS, Bernier L, Estevan J, Conejero G, Mongrand S, Fernandez D (2011) Identification and characterization of the Non-race specific Disease Resistance 1 (NDR1) orthologous protein in coffee. BMC Plant Biol 11:144
Cao H, Glazebrook J, Clarke JD, Volko S, Dong X (1997) The Arabidopsis NPR1 gene that controls systemic acquired resistance encodes a novel protein containing ankyrin repeats. Cell 88:57–63
Century KS, Shapiro AD, Repetti PP, Dahlbeck D, Holub E, Staskawicz BJ (1997) NDR1, a pathogen-induced component required for Arabidopsis disease resistance. Science 278:1963–1965
Cheng F, Liu S, Wu J, Fang L, Sun S, Liu B, Li P, Hua W, Wang X (2011) BRAD, the genetics and genomics database for Brassica plants. BMC Plant Biol 11:136
Daly P, Tomkins B (1995) Production and postharvest handling of Chinese cabbage (Brassica rapa var. pekinensis). RIRDC 97(1):41
Dangl JL, Jones JD (2001) Plant pathogens and integrated defence responses to infection. Nature 411:826–833
Diener AC (2013) Routine map** of Fusarium wilt resistance in BC1 populations of Arabidopsis thaliana. BMC Plant Biol 13:171
Diener AC, Ausubel FM (2005) RESISTANCE TO FUSARIUM OXYSPORUM 1, a dominant Arabidopsis disease-resistance gene, is not race specific. Genetics 171:305–321
Dodds PN, Rathjen JP (2010) Plant immunity: towards an integrated view of plant-pathogen interactions. Nat Rev Genet 11:539–548
Du Z, Zhou X, Ling Y, Zhang Z, Su Z (2010) agriGO: a GO analysis toolkit for the agricultural community. Nucleic Acids Res 38:W64–W70
Enya J, Togawa M, Takeuchi T, Yoshida S, Tsushima S, Arie T, Sakai T (2008) Biological and phylogenetic characterization of Fusarium oxysporum complex, which causes yellows on Brassica spp. And proposal of F. oxysporum f. sp. rapae, a novel forma specialis pathogenic on B. rapa in Japan. Phytopathology 98:475–483
Farnham MW, Keinath AP, Smith JP (2001) Characterization of fusarium yellows resistance in collard. Plant Dis 85:890–894
Ferrari S, Vairo D, Ausubel FM, Cervone F, De Lorenzo G (2003) Tandemly duplicated Arabidopsis genes that encode polygalacturonase-inhibiting proteins are regulated coordinately by different signal transduction pathways in response to fungal infection. Plant Cell 15:93–106
Ferrari S, Savatin DV, Sicilia F, Gramegna G, Cervone F, Lorenzo GD (2013) Oligogalacturonides: plant damage-associated molecular patterns and regulators of growth and development. Front Plant Sci 4:49
Fujimoto R, Sasaki T, Nishio T (2006) Characterization of DNA methyltransferase genes in Brassica rapa. Genes Genet Syst 81:235–242
Fujimoto R, Taylor JM, Shirasawa S, Peacock WJ, Dennis ES (2012) Heterosis of Arabidopsis hybrids between C24 and Col is associated with increased photosynthesis capacity. Proc Natl Acad Sci USA 109:7109–7114
Glazebrook J (2005) Contrasting mechanisms of defense against biotrophic and necrotrophic pathogens. Annu Rev Phytopathol 43:205–227
Hatakeyama K, Suwabe K, Tomita RN, Kato T, Nunome T, Fukuoka H, Matsumoto S (2013) Identification and characterization of Crr1a, a gene for resistance to clubroot disease (Plasmodiophora brassicae Woronin) in Brassica rapa L. PLoS One 8:e54745
Jones JD, Dangl JL (2006) The plant immune system. Nature 444:323–329
Joobeur T, King JJ, Nolin SJ, Thomas CE, Dean RA (2004) The Fusarium wilt resistance locus Fom-2 of melon contains a single resistance gene with complex features. Plant J 39:283–297
Joshi RK, Nayak S (2011) Functional characterization and signal transduction ability of nucleotide-binding site-leucine-rich repeat resistance genes in plants. Genet Mol Res 10:2637–2652
Lee SK, Song MY, Seo YS, Kim HK, Ko S, Cao PJ, Suh JP, Yi G, Roh JH, Lee S, An G, Hahn TR, Wang GL, Ronald P, Jeon JS (2009) Rice Pi5-mediated resistance to Magnaporthe oryzae requires the presence of two coiled-coil-nucleotide-binding-leucine-rich repeat genes. Genetics 181:1627–1638
Lei J, Wang D, Shao L, Wei X, Huang L (2012) Agrobacterium-mediated transformation of cotton shoot apex with SNC1 gene and resistance to cotton Fusarium wilt in T1 generation. Cotton Genomics Genet 3:1–7
Li X, Clarke JD, Zhang Y, Dong X (2001) Activation of an EDS1-mediated R-gene pathway in the snc1 mutant leads to constitutive, NPR1-independent pathogen resistance. Mol Plant Microbe Interact 14:1131–1139
Lu H, Zhang C, Albrecht U, Shimizu R, Wang G, Bowman KD (2013) Overexpression of a citrus NDR1 ortholog increases disease resistance in Arabidopsis. Front Plant Sci 4:157
Marone D, Russo MA, Laidò G, De Leonardis AM, Mastrangelo AM (2013) Plant nucleotide binding site–leucine-rich repeat (NBS–LRR) genes: active guardians in host defense responses. Int J Mol Sci 14:7302–7326
Meyers BC, Kozik A, Griego A, Kuang H, Michelmore RW (2003) Genome-wide analysis of NBS–LRR-encoding genes in Arabidopsis. Plant Cell 15:809–834
Murray MG, Thompson WF (1980) Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res 8:4321–4325
Muthamilarasan M, Prasad M (2013) Plant innate immunity: an updated insight into defense mechanism. J Biosci 38:433–449
Narusaka M, Shirasu K, Noutoshi Y, Kubo Y, Shiraishi T, Iwabuchi M, Narusaka Y (2009) RRS1 and RPS4 provide a dual Resistance-gene system against fungal and bacterial pathogens. Plant J 60:218–226
Okuyama Y, Kanzaki H, Abe A, Yoshida K, Tamiru M, Saitoh H, Fujibe T, Matsumura H, Shenton M, Galam DC, Undan J, Ito A, Sone T, Terauchi R (2011) A multifaceted genomics approach allows the isolation of the rice Pia-blast resistance gene consisting of two adjacent NBS–LRR protein genes. Plant J 66:467–479
Pu ZJ, Shimizu M, Zhang YJ, Nagaoka T, Hayashi T, Hori H, Matsumoto S, Fujimoto R, Okazaki K (2012) Genetic map** of a fusarium wilt resistance gene in Brassica oleracea. Mol Breed 30:809–818
Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425
Schneeberger K, Ossowski S, Lanz C, Juul T, Petersen AH, Nielsen KL, Jørgensen JE, Weigel D, Andersen SU (2009) SHOREmap: simultaneous map** and mutation identification by deep sequencing. Nat Methods 6:550–551
Seki M, Narusaka M, Kamiya A, Ishida J, Satou M, Sakurai T, Nakajima M, Enju A, Akiyama K, Oono Y, Muramatsu M, Hayashizaki Y, Kawai J, Carninci P, Itoh M, Ishii Y, Arakawa T, Shibata K, Shinagawa A, Shinozaki K (2002) Functional annotation of a full-length Arabidopsis cDNA collection. Science 296:141–145
Simons G, Groenendijk J, Wijbrandi J, Reijans M, Groenen J, Diergaarde P, Van der Lee T, Bleeker M, Onstenk J, de Both M, Haring M, Mes J, Cornelissen B, Zabeau M, Vos P (1998) Dissection of the fusarium I2 gene cluster in tomato reveals six homologs and one active gene copy. Plant Cell 10:1055–1068
Takagi H, Abe A, Yoshida K, Kosugi S, Natsume S, Mitsuoka C, Uemura A, Utsushi H, Tamiru M, Takuno S, Innan H, Cano LM, Kamoun S, Terauchi R (2013) QTL-seq: rapid map** of quantitative trait loci in rice by whole genome resequencing of DNA from two bulked populations. Plant J 74:174–183
Todesco M, Balasubramanian S, Hu TT, Traw MB, Horton M, Epple P, Kuhns C, Sureshkumar S, Schwartz C, Lanz C, Laitinen RA, Huang Y, Chory J, Lipka V, Borevitz JO, Dangl JL, Bergelson J, Nordborg M, Weigel D (2010) Natural allelic variation underlying a major fitness trade-off in Arabidopsis thaliana. Nature 465:632–636
Ueno H, Matsumoto E, Aruga D, Kitagawa S, Matsumura H, Hayashida N (2012) Molecular characterization of the CRa gene conferring clubroot resistance in Brassica rapa. Plant Mol Biol 80:621–629
Varet A, Hause B, Hause G, Scheel D, Lee J (2003) The Arabidopsis NHL3 gene encodes a plasma membrane protein and its overexpression correlates with increased resistance to Pseudomonas syringae pv. tomato DC3000. Plant Physiol 132:2023–2033
Walker JC (1930) Inheritance of fusarium resistance in cabbage. J Agric Res 40:721–745
Walker JC, Monteith J Jr, Wellman FL (1927) Development of three mid-season varieties of cabbage resistant to yellows (Fusarium conglutinans Woll.). J Agric Res 35:785–810
Wang X, Wang H, Wang J, Sun R, Wu J et al (2011) The genome of the mesopolyploid crop species Brassica rapa. Nat Genet 43:1035–1039
Yu X, Choi SR, Ramchiary N, Miao X, Lee SH, Sun HJ, Kim S, Ahn CH, Lim YP (2013) Comparative map** of Raphanus sativus genome using Brassica markers and quantitative trait loci analysis for the Fusarium wilt resistance trait. Theor Appl Genet 126:2553–2562
Zhang Y, Goritschnig S, Dong X, Li X (2003) A gain-of-function mutation in a plant disease resistance gene leads to constitutive activation of downstream signal transduction pathways in suppressor of npr1-1, constitutive 1. Plant Cell 15:2636–2646
Zhu Y, Du B, Qian J, Zou B, Hua J (2013) Disease resistance gene-induced growth inhibition is enhanced by rcd1 independent of defense activation in Arabidopsis. Plant Physiol 161:2005–2013
Acknowledgments
This work was supported in part by FY2012 Research Exchange Program between JSPS and AAS, by Grant-in-Aid for Young Scientists (B) (2478002) (JSPS), and Co-operative Research Programme 2012 (OECD) to R. Fujimoto, by Acorn Grant 2010 to R. Fujimoto and H. Ying, by Research Fellowships of JSPS for Young Scientists to M. Shimizu, and by the Programme for Promotion of Basic and Applied Researches for Innovations in Bio-oriented Industry to K. Okazaki.
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11103_2014_182_MOESM7_ESM.ppt
Figure S1. Schematic diagram of categorization of genes analyzed by RNA-seq. Number of putative disease resistance genes is shown in parentheses. Red letters show the numbers of putative R-genes showing two-fold differential expression level with 95% confidence. Blue letters show the numbers of putative R-genes showing only a two-fold differential expression level without 95% confidence or no expression in either line. (PPT 184 kb)
11103_2014_182_MOESM8_ESM.ppt
Figure S2. Summary of 244 putative R-genes having NBS, LRR, TIR, or CC motifs sub-categorized into 16 categorizes (sited from Brassica database). (PPT 228 kb)
11103_2014_182_MOESM9_ESM.ppt
Figure S3. Deletion of Bra012688 and Bra012689 in fusarium yellows susceptible line. Boxes show exon regions. Red, blue, and green bars show the region tested by PCR using genomic DNAs as templates. The result of PCR is shown in bottom panel. 23, RJKB-T23; 24, RJKB-T24 (PPT 258 kb)
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Shimizu, M., Fujimoto, R., Ying, H. et al. Identification of candidate genes for fusarium yellows resistance in Chinese cabbage by differential expression analysis. Plant Mol Biol 85, 247–257 (2014). https://doi.org/10.1007/s11103-014-0182-0
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DOI: https://doi.org/10.1007/s11103-014-0182-0