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Genetic linkage maps of rose constructed with new microsatellite markers and locating QTL controlling flowering traits

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Abstract

New microsatellites markers [simple sequence repeat (SSR)] have been isolated from rose and integrated into an existing amplified fragment-length polymorphism genetic map. This new map was used to identify quantitative trait locus (QTL) controlling date of flowering and number of petals. From a rose bud expressed sequence tag (EST) database of 2,556 unigenes and a rose genomic library, 44 EST-SSRs and 20 genomic-SSR markers were developed, respectively. These new rose SSRs were used to expand genetic maps of the rose interspecific F1 progeny. In addition, SSRs from other Rosaceae genera were also tested in the mapping progeny. Genetic maps for the two parents of the progeny were constructed using pseudo-testcross mapping strategy. The maps consist of seven linkage groups of 105 markers covering 432 cM for the maternal map and 136 markers covering 438 cM for the paternal map. Homologous relationships among linkage groups between the maternal and paternal maps were established using SSR markers. Loci controlling flowering traits were localised on genetic maps as a major gene and QTL for the number of petals and a QTL for the blooming date. New SSR markers developed in this study will provide tools for the establishment of a consensus linkage map for roses that combine traits and markers in various rose genetic maps.

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References

  • Aranzana MJ, Pineda A, Cosson P, Dirlewanger E, Ascasibar J, Cipriani G, Ryder CD, Testolin R, Abbott A, King GJ, Iezzoni AF, Arus P (2003) A set of simple-sequence repeat (SSR) markers covering the Prunus genome. Theor Appl Genet 106:819–825

    PubMed  CAS  Google Scholar 

  • Blair MW, Pedraza F, Buendia HF, Gaitan-Solis E, Beebe SE, Gepts P, Tohme J (2003) Development of a genome-wide anchored microsatellite map for common bean (Phaseolus vulgaris L.). Theor Appl Genet 107:1362–1374

    Article  PubMed  CAS  Google Scholar 

  • Blom TJ, Tsujita MJ (2003) Cut rose production. In: Roberts AV, Debener T, Gudin S (eds) Encyclopedia of rose science, vol 2. Elsevier Academic Press, Oxford, pp 594–600

    Google Scholar 

  • Channeliere S, Riviere S, Scalliet G, Szecsi J, Jullien F, Dolle C, Vergne P, Dumas C, Mohammed B, Hugueney P, Cock JM (2002) Analysis of gene expression in rose petals using expressed sequence tags. FEBS Lett 515:35–38

    Article  PubMed  CAS  Google Scholar 

  • Cho YG, Ishii T, Temnykh S, Chen X, Lipovich L, McCouch SR, Park WD, Ayres N, Cartinhour S (2000) Diversity of microsatellites derived from genomic libraries and GenBank sequences in rice (Oryza sativa L.). Theor Appl Genet 100:713–722

    Article  CAS  Google Scholar 

  • Crespel L, Chirollet M, Durel CE, Zhang D, Meynet J, Gudin S (2002) Mapping of qualitative and quantitative phenotypic traits in Rosa using AFLP markers. Theor Appl Genet 105:1207–1214

    Article  PubMed  CAS  Google Scholar 

  • Creste S, Tulman Neto A, Figueira A (2001) Detection of single sequence repeat polymorphisms in denaturing polyacrylamide sequencing gels by silver staining. Plant Mol Biol Report 19:299–306

    CAS  Google Scholar 

  • Debener T (1999) Genetic analysis of horticulturally important morphological and physiological characters in diploid roses. Gartenbauwissenschaft 64:14–20

    Google Scholar 

  • Debener T, Mattiesch L (1999) Construction of a genetic linkage map for roses using RAPD and AFLP markers. Theor Appl Genet 99:891–899

    Article  CAS  Google Scholar 

  • Debener T, Von Malek B, Mattiesch L, Kaufmann H (2001) Genetic and molecular analysis of important characters in roses. Acta Hortic 547:45–49

    CAS  Google Scholar 

  • Dickson EE, Arumuganathan K, Kresovich S, Doyle J (1992) Nuclear DNA content variation within the Rosaceae. Am J Bot 79:1081–1086

    Article  Google Scholar 

  • Dirlewanger E, Cosson P, Tavaud M, Poizat C, Moing A, Zanetto A, Aranzana MJ, Arus P (2002) Development of peach SSRs and their use in fingerprinting peach and sweet cherry cultivars. Acta Hortic 592:245–252

    Google Scholar 

  • Dugo ML, Satovic Z, Millan T, Cubero JI, Rubiales D, Cabrera A, Torres AM (2005) Genetic mapping of QTLs controlling horticultural traits in diploid roses. Theor Appl Genet 111:511–520

    Article  PubMed  CAS  Google Scholar 

  • Echt CS, May-Marquardt P (1997) Survey of microsatellite DNA in pine. Genome 40:9–17

    PubMed  CAS  Google Scholar 

  • Esselink GD, Smulders MJM, Vosman B (2003) Identification of cut rose (Rosa hybrida) and rootstock varieties using robust sequence tagged microsatellite site markers. Theor Appl Genet 106:277–286

    PubMed  CAS  Google Scholar 

  • Fulton TM, van der Hoeven R, Eannetta NT, Tanksley SD (2002) Identification, analysis, and utilization of conserved ortholog set markers for comparative genomics in higher plants. Plant Cell 14:1457–1467

    Article  PubMed  CAS  Google Scholar 

  • Gudin S (2000) Rose: genetics and breeding. Plant Breed Rev 17:159–189

    CAS  Google Scholar 

  • Guterman I, Shalit M, Menda N, Piestun D, Dafny-Yelin M, Shalev G, Bar E, Davydov O, Ovadis M, Emanuel M, Wang JH, Adam Z, Pichersky E, Lewinsohn E, Zamir D, Vainstein A, Weiss D (2002) Rose scent: genomics approach to discovering novel floral fragrance-related genes. Plant Cell 14:2325–2328

    Article  PubMed  CAS  Google Scholar 

  • Huang S, Zhang B, Milbourne D, Cardle L, Yang G, Guo J (2001) Development of pepper SSR markers from sequence databases. Euphytica 117:163–167

    Article  CAS  Google Scholar 

  • Jung S, Abbott A, Jesudurai C, Tomkins J, Main D (2005) Frequency, type, distribution and annotation of simple sequence repeats in Rosaceae ESTs. Funct Integr Genomics 5:139–143

    Google Scholar 

  • Kantety RV, Rota Ml, Matthews DE, Sorrells ME (2002) Data mining for simple sequence repeats in expressed sequence tags from barley, maize, rice, sorghum and wheat. Plant Mol Biol 48:501–510

    Article  PubMed  CAS  Google Scholar 

  • Liebhard R, Koller B, Gianfranceschi L, Gessler C (2003) Creating a saturated reference map for the apple (Malus × domestica Borkh.) genome. Theor Appl Genet 106:1497–1508

    PubMed  CAS  Google Scholar 

  • Linde M, Mattiesch L, Debener T (2004) Rpp1, a dominant gene providing race-specific resistance to rose powdery mildew (Podosphaera pannosa): molecular mapping, SCAR development and confirmation of disease resistance data. Theor Appl Genet 109:1261–1266

    Article  PubMed  CAS  Google Scholar 

  • Malek BV, Weber WE, Debener T (2000) Identification of molecular markers linked to Rdr1, a gene conferring resistance to blackspot in roses. Theor Appl Genet 101:977–983

    Article  Google Scholar 

  • Marie D, Brown SC (1993) A cytometric exercise in plant DNA histograms, with 2C values for 70 species. Biol Cell 78:41–51

    Article  PubMed  CAS  Google Scholar 

  • Meynet J, Barrade R, Duclos A, Siadous R (1994) Dihaploid plants of roses (Rosa × hybrida, cv ‘Sonia’) obtained by parthenogenesis induced using irradiated pollen and in vitro culture of immature seeds. Agronomie 14:169–175

    Article  Google Scholar 

  • Morgante M, Olivieri AM (1993) PCR-amplified microsatellites as markers in plant genetics. Plant J 3:175–182

    Article  PubMed  CAS  Google Scholar 

  • Morgante M, Hanafey M, Powell W (2002) Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes. Nat Genet 30:194–200

    Article  PubMed  CAS  Google Scholar 

  • Nicot N, Chiquet V, Gandon B, Amilhat L, Legeai F, Leroy P, Bernard M, Sourdille P (2004) Study of simple sequence repeat (SSR) markers from wheat expressed sequence tags (ESTs). Theor Appl Genet 109:800–805

    Article  PubMed  CAS  Google Scholar 

  • Nybom H, Esselink GD, Werlemark G, Vosman B (2004) Microsatellite DNA marker inheritance indicates preferential pairing between two highly homologous genomes in polyploid and hemisexual dog-roses, Rosa L. sect. Caninae DC. Heredity 92:139–150

    Article  PubMed  CAS  Google Scholar 

  • Panaud O, Chen X, McCouch SR (1996) Development of microsatellite markers and characterization of simple sequence length polymorphism (SSLP) in rice (Oryza sativa L.). Mol Gen Genet 252:597–607

    PubMed  CAS  Google Scholar 

  • Put HMC, Clerkx ACM (2003) Xylem structure and function of cut roses. In: Roberts AV, Debener T, Gudin S (eds) Encyclopedia of rose science, vol 2. Elsevier Academic Press, Oxford, pp 529–549

    Google Scholar 

  • Rajapakse S, Byrne DH, Zhang L, Anderson N, Arumuganathan K, Ballard RE (2001) Two genetic linkage maps of tetraploid roses. Theor Appl Genet 103:575–583

    Article  CAS  Google Scholar 

  • Rozen S, Skaletsky HJ (2000) Primer3 on the WWW for general users and for biologist programmers. In: Krawetz S, Misener S (eds) Bioinformatics methods and protocols: methods in molecular biology. Humana Press, Totowa, NJ, pp 365–386

    Google Scholar 

  • Rusanov K, Kovacheva N, Vosman B, Zhang L, Rajapakse S, Atanassov A, Atanassov I (2005) Microsatellite analysis of Rosa damascena Mill. accessions reveals genetic similarity between genotypes used for rose oil production and old Damask rose varieties. Theor Appl Genet 111:804–809

    Article  PubMed  CAS  Google Scholar 

  • Sargent DJ, Davis TM, Tobutt KR, Wilkinson MJ, Battey NH, Simpson DW (2004) A genetic linkage map of microsatellite, gene-specific and morphological markers in diploid Fragaria. Theor Appl Genet 109:1385–1391

    Article  PubMed  CAS  Google Scholar 

  • Schloss SJ, Mitchell SE, White GM, Kukatla R, Bowers JE, Paterson AH, Kresovich S (2002) Characterization of RFLP probe sequences for gene discovery and SSR development in Sorghum bicolor (L.) Moench. Theor Appl Genet 105:912–920

    Article  PubMed  CAS  Google Scholar 

  • Schulke M (2000) An economic method for the fluorescent labeling of PCR fragments. Nat Amat 18:233–234

    Google Scholar 

  • Scott KD, Eggler P, Seaton G, Rossetto M, Ablett EM, Lee LS, Henry RJ (2000) Analysis of SSRs derived from grape ESTs. Theor Appl Genet 100:723–726

    Article  CAS  Google Scholar 

  • Sosinski B, Gannavarapu M, Hager LD, Beck LE, King GJ, Ryder CD, Rajapakse S, Baird WV, Ballard RE, Abbott AG (2000) Characterization of microsatellite markers in peach (Prunus persica (L.) Batsch). Theor Appl Genet 101:421–428

    Article  CAS  Google Scholar 

  • Stam P (1993) Construction of integrated genetic linkage maps by means of a new computer package: JOINMAP. Plant J 3:739–744

    Article  CAS  Google Scholar 

  • Van Ooijen JW, Maliepaard C (1997) MapQTL version 3.0: software for the calculation of QTL positions on genetic maps. In: Advances in biometrical genetics. Proceedings of the tenth meeting of the EUCARPIA Section Biometrics in Plant Breeding, Poznan, Poland, 14–16 May 1997

  • Vuylsteke M, Mank R, Antonise R, Bastiaans E, Senior ML, Stuber CW, Melchinger AE, Lubberstedt T, Xia XC, Stam P, Zabeau M, Kuiper M (1999) Two high-density AFLP(R) linkage maps of Zea mays L.: analysis of distribution of AFLP markers. Theor Appl Genet 99:921–935

    Article  CAS  Google Scholar 

  • Wang Y, Georgi LL, Zhebentyayeva TN, Reighard GL, Scorza R, Abbott AG (2002) High-throughput targeted SSR marker development in peach (Prunus persica). Genome 45:319–328

    Article  PubMed  CAS  Google Scholar 

  • Wissemann V (2003) Classification. In: Roberts AV, Debener T, Gudin S (eds) Encyclopedia of rose science, vol 1. Elsevier Academic Press, Oxford, pp 111–117

    Google Scholar 

  • Wylie AP (1954) The history of garden roses. Masters memorial lecture 1954. J R Hortic Soc 79:555–571

    Google Scholar 

  • Yan Z, Denneboom C, Hattendorf A, Dolstra O, Debener T, Stam P, Visser PB (2005) Construction of an integrated map of rose with AFLP, SSR, PK, RGA, RFLP, SCAR and morphological markers. Theor Appl Genet 110:766–777

    Article  PubMed  CAS  Google Scholar 

  • Yokoya K, Roberts AV, Mottley J, Lewis R, Brandham PE (2000) Nuclear DNA amounts in roses. Ann Bot 85:557–561

    Article  CAS  Google Scholar 

  • Zhang LH, Byrne DH, Ballard RE, Rajapakse S (2006) Microsatellite marker development in rose and its application in tetraploid mapping. J Am Soc Hortic Sci 131(3):380–387

    Article  CAS  Google Scholar 

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Acknowledgement

We thank Ouest-Genopole® for sequencing and genotyping works and the development of bio-informatic tools for SSR detection. The authors gratefully acknowledge D. Lalanne for technical assistance, M.E. Plouteau and J. Nassibou for their participation in the mapping work, C. Foubert, C. Brouard and Y. Rabineau for growing the plants and B. Denoyes-Rothan (INRA, Bordeaux) for providing us F3-7C SSR primers. We also thank T. Debener and A. Pernet for critical reading of the manuscript. This work was partly supported by specific funding from the Institut National de la Recherche Agronomique.

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Author notes

  1. S. Rajapakse

    Present address: Department of Biology, Greenville Technical College, Greenville, SC, 29606, USA

  2. L. Zhang

    Present address: IAREC, Washington State University, Prosser, WA, 99350, USA

Authors and Affiliations

  1. UMR GenHort (Génétique et Horticulture), INRA, BP 60057, 49071, Beaucouzé, France

    L. Hibrand-Saint Oyant & F. Foucher

  2. Ets Meilland, Quart St André 83340, Le Cannet des Maures, France

    L. Crespel

  3. Department of Genetics and Biochemistry, Clemson University, Clemson, SC, 29634, USA

    S. Rajapakse & L. Zhang

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  1. L. Hibrand-Saint Oyant
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  3. S. Rajapakse
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  4. L. Zhang
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Correspondence to L. Hibrand-Saint Oyant.

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Communicated by A. Abbott

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Hibrand-Saint Oyant, L., Crespel, L., Rajapakse, S. et al. Genetic linkage maps of rose constructed with new microsatellite markers and locating QTL controlling flowering traits. Tree Genetics & Genomes 4, 11–23 (2008). https://doi.org/10.1007/s11295-007-0084-2

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  • DOI: https://doi.org/10.1007/s11295-007-0084-2

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