Abstract
Pathogenesis-related (PR) genes were isolated from chestnut rose (Rosa roxburghii Tratt) using a PCR approach with degenerate primers designed for the conserved regions of two PR gene families: class 2 (β-1,3-glucanase) and class 5 (osmotin). Thirteen PR2 and ten PR5 genes were obtained, with a nucleotide identity that ranged from 40.1 to 99.7% and from 99.2 to 99.8%, respectively. Sequence comparison revealed the presence of single nucleotide polymorphisms (SNPs) in these sequences with, on an average, one SNP in every 64-bp fragment for the PR2 genes and one in every 68-bp fragment for the PR5 genes. A total of 23 primers were used to genotype these SNPs for use in developing single nucleotide-amplified polymorphisms (SNAP) markers. One marker (Glu7) was found to be linked to powdery mildew resistance loci. Based on genetic mapping of a segregating F1 population, we determined that 16 of the 23 SNAP markers formed one group and subsequently detected a quantitative trait locus that accounted for 12% of the variation in the powdery mildew resistance phenotype. The results of this study provide a first insight into the genomic structure of PR genes and show that the candidate gene approach in combination with SNAP markers is an attractive strategy to search for powdery mildew resistance loci in chestnut rose.
Similar content being viewed by others
References
Alexander D, Goodman RM, Gut-Rella M, Glascock C, Weymann K, Friedrich L, Maddox D, Ahl-Goy P, Luntz T, Ward E, Ryals J (1993) Increased tolerance to two oomycete pathogens in transgenic tobacco expressing pathogenesis-related protein 1a. Proc Natl Acad Sci USA 90:7327–7331
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programmes. Nucleic Acids Res 25:3389–3402
Batley J, Barker G, O’Sullivan H, Edwards KJ, Edwards D (2003) Mining for single nucleotide polymorphisms and insertions/deletions in maize expressed sequence tag data. Plant Physiol 132:84–91
Bergelson J, Kreitman M, Stahl EA, Tian D (2001) Evolutionary dynamics of plant R-genes. Science 292:2281–2285
Bishop JG, Dean AM, Mitchell-Olds T (2000) Rapid evolution in plant chitinases: molecular targets of selection in plant–pathogen coevolution. Proc Natl Acad Sci USA 97:5322–5327
Dangl JL, Jones JDG (2001) Plant pathogens and integrated defence responses to infection. Nature 411:826–833
Delye C, Calmes E, Matejicek A (2002) SNP markers for black-grass (Alopecurus myosuroides Huds.) genotypes resistant to acetyl CoA-carboxylase inhibiting herbicides. Theor Appl Genet 104:1114–1120
Drenkard E, Richter BG, Rozen S, Stutius LM, Angell NA, Mindrinos M, Cho RJ, Oegner PJ, Davis RW, Ausubel FM (2000) A simple procedure for the analysis of single nucleotide polymorphisms facilitates map-based cloning in Arabidopsis. Plant Physiol 124:1483–1492
Faris JD, Li W, Gill BS, Liu D, Chen P (1999) Candidate gene analysis of quantitative disease resistance in wheat. Theor Appl Genet 98:219–225
Foulongne M, Pascal T, Pfeiffer F, Kervella J (2003) QTLs for powdery mildew in peach × Prunus davidiana crosses: consistency across generations and environments. Mol Breed 12:33–50
Hayashi K, Hashimoto N, Daigen M, Ashikawa I (2004) Development of PCR-based SNP markers for rice blast resistance genes at the Piz locus. Theor Appl Genet 108:1212–1220
Geoffroy V, Sevignac M, de Oliveira J, Fouilloux G, Skroch P, Thoquet P, Gepts P, Langin T, Dron M (2000) Inheritance of partial resistance against Colletrotichum lindemuthianum in Phaseolus vulgaris and co-localization of quantitative trait loci with genes involved in specific resistance. Mol Plant-Microbe Interact 13:287–296
Jander G, Norris SR, Rounsley SD, Bush DF, Levin IM, Last RL (2002) Arabidopsis map-based cloning in the post-genome era. Plant Physiol 129:440–450
Kanazin V, Talbert H, See D, DeCamp P, Nevo E, Blake T (2002) Discovery and assay of single-nucleotide polymorphisms in barley (Hordeum vulgare). Plant Mol Biol 48:529–537
Kim MY, Van K, Lestari P, Moon JK, Lee SH (2005) SNP identification and SNAP marker development for a GmNARK gene controlling supernodulation in soybean. Theor Appl Genet 110:1003–1010
Kumar S, Tamura K, Nei M (2004) MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 5:150–163
Lanaud C, Risterucci AM, Pieretti I, N’Goran JAK, Fargeas D (2004) Characterization and genetic mapping of resistance and defence gene analogs in coca (Theobroma cacao L.). Mol Breed 13:211–227
Lawton KA, Friedrich L, Hunt M, Weymann K, Delaney TP, Kessmann H, Staub T, Ryals J (1996) Benzothiadiazole induces disease resistance in Arabidopsis by activation of the systemic acquired resistance signal transduction pathway. Plant J 10:71–82
Leonards-Schippers C, Gieffers W, Schafer-Pregl R, Ritter E, Knapp SJ, Salamini F, Gebhardt C (1994) Quantitative resistance to Phytophthora infestans in potato: a case study for QTL mapping in an allogamous plant species. Genetics 137:67–77
Liu D, Raghothama KG, Hasegawa PM, Bressan RA (1994) Osmotin overexpression in potato delays development of disease symptoms. Proc Natl Acad Sci USA 91:1888–1892
Ma YX, Zhu Y, Wang CF (1997) The aging retarding effect of ‘Long-Life CiLi’. Mech Ageing Dev 96:171–189
Meer J, Cudmore R, Manly KF (2004) Map manager QTX. (http://www.mapmanager.org/mmQTX.html)
Michelmore RW, Meyers BC (1998) Clusters of resistance genes in plants evolve by divergent selection and a birth-and-death process. Genome Res 8:1113–1130
Mondragon-palomino M, Meyers BC, Michelmore RW, Gaut BS (2002) Patterns of positive selection in the complete NBS-LRR gene family of Arabidopsis thaliana. Genome Res 12:1305–1315
Neale AD, Wahleithner JA, Lund M, Bonnett HT, Kelly A, Meekswagner DR, Peacock WJ, Dennis ES (1990) Chitinase, beta-1,3-glucanase, osmotin, and extensin are expressed in tobacco explants during flower formation. Plant Cell 2:673–684
Nei M, Gojobori T (1986) Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol 3:418–426
Pflieger S, Lefebvre V, Causse M (2001a) The candidate gene approach in plant genetics: a review. Mol Breed 7:275–291
Pflieger S, Palloix A, Caranta C, Blattes A, Lefebvre V (2001b) Defense response genes co-localize with quantitative disease resistance loci in pepper. Theor Appl Genet 103:920–929
Ponstein AS, Bres-Vloemans SA, Sela-Buurlage MB, van den Elzen PJM, Melchers LS, Cornelissen BJC (1994) A novel pathogen- and wound-inducible tobacco (Nicotiana tabacum) protein with antifungal activity. Plant Physiol 104:109–118
Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: a laboratory manual, 2nd edn. Cold Spring Harbour Laboratory, Plainview
van Kan JAL, Joosten MHAJ, Wagemakers CAM, van den Berg-Velthuis GCM, de Wit PJGM (1992) Differential accumulation of mRNAs encoding extracellular and intracellular PR proteins in tomato induced by virulent and avirulent races of Cladosporium fulvum. Plant Mol Biol 20:513–527
van Loon LC, van Strien EA (1999) The families of pathogenesis-related proteins, their activities, and comparative analysis of PR-1 type proteins. Phys Mol Plant Pathol 55:85–97
Wen XP, Deng XX (2005) Micropropagation of chestnut rose (Rosa roxburghii Tratt) and genetic stability assessment of the in vitro plants using RAPD and AFLP markers. J Hortic Sci Biotechnol 80:54–60
Xu Q, Wen XP, Deng XX (2005) Isolation of TIR and NonTIR NBS-LRR resistance gene analogues and identification of molecular markers linked to a powdery mildew resistance locus in chestnut rose (Rosa roxburghii Tratt). Theor Appl Genet 111:819–830
Young ND (2000) The genetic architecture of resistance. Curr Opin Plant Biol 3:285–290
Yu J, Hu S, Wang J, et al (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296:79–92
Zhu YL, Song QJ, Hyten DL, Van Tassell CP, Matukumalli LK,Grimm DR, Hyatt SM, Fickus EW, Young ND, Cregan PB (2003) Single-nucleotide polymorphisms in soybean. Genetics 163:1123–1134
Acknowledgements
This project was support by the National Natural Science Foundation of China (NSFC) (Nos. 30260070, 30123001 and 30471201), the IRT0548 of MOE. We are grateful to two anonymous reviewers for their helpful comments; thanks are also extended to Dr. Gerald Martin from The Center for Medicinal Plants Research in India and Dr. Guo in our laboratory.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Xu, Q., Wen, X. & Deng, X. Cloning of two classes of PR genes and the development of SNAP markers for powdery mildew resistance loci in chestnut rose (Rosa roxburghii Tratt). Mol Breeding 19, 179–191 (2007). https://doi.org/10.1007/s11032-006-9058-6
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s11032-006-9058-6