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EST-SSR genetic maps for Citrus sinensis and Poncirus trifoliata

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Abstract

The segregation of 141 polymorphic expressed sequence tag-simple sequence repeat (EST-SSR) markers in an F1 intergeneric citrus population was studied to build the first extensive EST maps for the maternal sweet orange and paternal Poncirus genomes. Of these markers, 122 were found segregating in sweet orange, 59 in Poncirus, and 40 in both. Eleven linkage groups with 113 markers in sweet orange, 8 with 45 markers in Poncirus, and 13 with 123 markers in the cross pollinator (CP) consensus of both, were constructed. About 775.8 cM of sweet orange genome and 425.7 cM of Poncirus genome were covered. Through comparison of shared markers, three cases were found where two linkage groups in one map apparently were colinear with one group of the other map; Poncirus linkages Ar1a and Ar1b and consensus linkages CP1a and CP1b, were both collinear with one sweet orange linkage, Sa1, as were sweet orange Sa3a and Sa3b with Poncirus Ar3 and consensus CP3, and sweet orange Sa7a and Sa7b, and consensus CP7a and CP7b with Poncirus Ar7. These EST-SSR markers are particularly useful for constructing comparative framework maps for related genera because they amplify orthologous genes to provide anchor points across taxa. All SSR primers are freely available to the citrus community.

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References

  • Ahmad R, Struss D, Southwick SM (2003) Development and characterization of microsatellite markers in Citrus. J Am Soc Hortic Sci 128:584–590

    CAS  Google Scholar 

  • Arumuganathan K, Earle ED (1991) Nuclear DNA content of some important plant species. Plant Mol Biol Rep 9:208–218

    CAS  Google Scholar 

  • Bernet GP, Margaix C, Jacas J, Carbonell EA, Asins MJ (2005) Genetic analysis of citrus leafminer susceptibility. Theor Appl Genet 110:1393–1400

    Article  PubMed  CAS  Google Scholar 

  • Cai Q, Guy CL, Moore GA (1994) Extension of the genetic linkage map in Citrus using random amplified polymorphic DNA (RAPD) markers and RFLP mapping of cold-acclimation responsive loci. Theor Appl Genet 89:606–614

    Article  CAS  Google Scholar 

  • Cameron JW, Soost RK (1984) Citrus. In: Simmonds NW (ed) Evolution of crop plants. Logman, New York, pp 261–264

    Google Scholar 

  • Chen C, Zhou P, Choi YA, Huang S, Gmitter Jr FG (2006a) Mining and characterizing microsatellites from citrus ESTs. Theor Appl Genet 112:1248–1257

    Article  PubMed  CAS  Google Scholar 

  • Chen C, Burrage AD, Choi YA, Soneji JR, Rao MN, Huang S, Gmitter Jr FG (2006b) Aligning citrus unigenes with Arabidopsis and rice chromosome sequences. Plant & Animal Genomes XIV Conference, San Diego, CA, USA, p 97

  • Cheng FS, Roose ML (1995) Origin and inheritance of dwarfing by citrus rootstock Poncirus trifoliata ‘Flying Dragon’. J Am Soc Hortic Sci 120:286–291

    Google Scholar 

  • Choi YA, Chen C, Huang S, Gmitter FG Jr (2005) Quantitative trait linkage (QTL) mapping for resistance to citrus canker within Citrus. The 2nd International Canker/Huanlongbin Workshop, Orlando, FL, USA, Poster 10

  • Close TJ, Wanamaker S, Lyon M, Mei GW, Davies C, Roose ML (2006) A genechip® for citrus. In: Plant & Animal Genomes XIV Conf, San Diego, CA, USA, Workshop, p 82

  • Cristofani M, Machado MA, Grattapaglia D (1999) Genetic linkage maps of Citrus sunki Hort. ex. Tan. and Poncirus trifoliata (L.) Raf. and mapping of citrus tristeza virus resistance gene. Euphytica 109:25–32

    Article  CAS  Google Scholar 

  • Dalkilic Z, Timmer LW, Gmitter FG Jr (2005) Linkage of Alternaria disease resistance gene in mandarin hybrids with RAPD fragments. J Am Soc Hortic Sci 130:191–195

    CAS  Google Scholar 

  • Deng Z, Huang S, Xiao S, Gmitter FG Jr (1997) Development and characterization of SCAR markers linked to the citrus tristeza virus resistance gene from Poncirus trifoliata. Genome 40:697–704

    CAS  Google Scholar 

  • Deng Z, Huang S, Ling P, Yu C, Tao Q, Chen C, Wendell MK, Zhang HB, Gmitter FG Jr (2001) Fine genetic mapping and BAC contig development for the citrus tristeza virus resistance gene locus in Poncirus trifoliata (Raf.). Mol Genet Genomics 265:739–747

    Article  PubMed  CAS  Google Scholar 

  • Durham RE, Liou PC, Gmitter Jr FG, Moore GA (1992) Linkage of restriction fragment length polymorphisms and isozymes in Citrus. Theor Appl Genet 84:39–48

    Article  CAS  Google Scholar 

  • Fang DQ, Federici CT, Roose ML (1997) Development of molecular markers linked to a gene controlling fruit acidity in citrus. Genome 40:841–849

    CAS  Google Scholar 

  • Fang DQ, Federici CT, Roose ML (1998) A high-resolution linkage map of the citrus tristeza virus resistance gene region in Poncirus trifoliata (L.) Raf. Genetics 150:883–890

    PubMed  CAS  Google Scholar 

  • Garcia R, Asins MJ, Forner J, Carbonell EA (1999) Genetic analysis of apomixis in Citrus and Poncirus by molecular markers. Theor Appl Genet 99:511–518

    Article  CAS  Google Scholar 

  • Garcia R, Asins MJ, Carbonell EA (2000) QTL analysis of yield and seed number in Citrus. Theor Appl Genet 101:487–493

    Article  CAS  Google Scholar 

  • Gmitter FG Jr (1994) Contemporary approaches to improving citrus cultivars. HortTechnology 4:206–210

    Google Scholar 

  • Gmitter FG Jr, Xiao SY, Huang S, Hu XL, Garnsey SM, Deng Z (1996) A localized linkage map of the citrus tristeza virus resistance gene region. Theor Appl Genet 92:688–695

    Article  CAS  Google Scholar 

  • Gonzalo MJ, Oliver M, Garcia-Mas J, Monfort A, Dolcet-Sanjuan R, Katzir N, Arus P, Monforte AJ (2005) Simple-sequence repeat markers used in merging linkage maps of melon (Cucumis melo L.). Theor Appl Genet 110:802–811

    Article  PubMed  CAS  Google Scholar 

  • Grattapaglia D, Sederoff R (1994) Genetic linkage maps of Eucalyptus grandis and Eucalyptus urophylla using a pseudo-testcross: mapping strategy and RAPD markers. Genetics 137:1121–1137

    PubMed  CAS  Google Scholar 

  • Hulbert SH, Ilott TW, Legg EJ, Lincoln SE, Lander ES, Michelmore RW (1988) Genetic analysis of the fungus, Bremia lactucae, using restriction fragment length polymorphisms. Genetics 120:947–958

    PubMed  CAS  Google Scholar 

  • Jarrell DC, Roose ML, Traugh SN, Kupper RS (1992) A genetic map of citrus based on the segregation of isozymes and RFLPs in an intergeneric cross. Theor Appl Genet 84:49–56

    Article  CAS  Google Scholar 

  • Kepiro JL, Roose ML (2000) Molecular genetic analysis of nucellar embryony (apomixis) in Citrus maxima X Poncirus trifoliata using AFLP. In: Proc Intl Soc Citricult, Vol 1, 3–7 Dec, 2000, Orlando, Florida, USA, p 212

  • Kijas JM, Fowler JC, Thomas MR (1995) An evaluation of sequence tagged microsatellite site markers for genetic analysis within Citrus and related species. Genome 38:349–355

    PubMed  CAS  Google Scholar 

  • Kijas JMH, Thomas MR, Fowler JCS, Roose ML (1997) Integration of trinucleotide microsatellites into a linkage map of Citrus. Theor Appl Genet 94:701–706

    Article  CAS  Google Scholar 

  • Lander ES, Green P, Abrahamson J, Barlow A, Daley M, Lincoln S, Newburg L (1987) MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1:174–181

    Article  PubMed  CAS  Google Scholar 

  • Ling P, Yu C, Deng Z, Chen C, Huang S, Wendell MK, Gmitter Jr FG (1999) Citrus genome mapping with AFLP markers. In: Plant & Animal Genomes XIII Conf, San Diego, CA, USA, Poster 189

  • Ling P, Duncan LW, Deng Z, Dunn D, Xu X, Huang S, Gmitter Jr FG (2000) Inheritance of citrus nematode resistance and its linkage with molecular markers. Theor Appl Genet 101:1010–1017

    Article  Google Scholar 

  • Liou PC (1990) A molecular study of the Citrus genome through analysis of restriction fragment length polymorphism and isozyme mapping. Ph.D. Dissertation. University of Florida, Gainseville, USA

  • Lodhi MA, Daly MJ, Ye GN, Weeden NF, Reisch BI (1995) A molecular marker based linkage map of Vitis. Genome 38:786–794

    PubMed  CAS  Google Scholar 

  • Luro F, Laigret F, Lorieux M, Ollitrault P (1996) Citrus genome mapping with molecular markers: two maps obtained by segregation analysis of progeny of one intergeneric cross. Proc Intl Soc Citricult 2:862–866

    Google Scholar 

  • Nicolosi E, Deng ZN, Gentile A, La Malfa S, Continella G, Tribulato E (2000) Citrus phylogeny and genetic origin of important species as investigated by molecular markers. Theor Appl Genet 100:1155–1166

    Article  CAS  Google Scholar 

  • de Oliveira RP, Cristofani M, Machado MA (2002) Genetic mapping for citrus variegated chlorosis resistance. Laranja 23:247–261

    Google Scholar 

  • Omura M, Ueda T, Kita M, Komatsu A, Takanokura Y, Shimada T, Endo-Inagaki T, Nesumi H, Yoshida T (2000) EST Mapping of Citrus. Proceedings of the International Society of Citriculture IX Congress. Orlando, FL, USA. pp 71–74

  • Ritter E, Gebhardt C, Salamini F (1990) Estimation of recombination frequencies and construction of RFLP linkage maps in plants from crosses between heterozygous parents. Genetics 125:645–654

    PubMed  CAS  Google Scholar 

  • Roose ML, Fang D, Cheng FS, Tayyar RI, Federici CT, Kupper RS (2000) Mapping the citrus genome. In: Goren R, Goldschmidt EE (eds) Proc Intl Soc Hort Sci (ISHS). Leuven, Belgium, Acta Hort 535:25–32

  • Ruiz C, Asins MJ (2003) Comparison between Poncirus and Citrus genetic linkage maps. Theor Appl Genet 106:826–836

    PubMed  CAS  Google Scholar 

  • Sankar AA, Moore GA (2001) Evaluation of inter-simple sequence repeat analysis for mapping in Citrus and extension of the genetic linkage map. Theor Appl Genet 102:206–214

    Article  CAS  Google Scholar 

  • Scora RW (1988) Biochemistry, taxonomy and evolution of modern cultivated citrus. In: Goren R, Mendel K (eds) Citriculture. Proc Intl Soc Citricult, pp 227–289

  • de Simone M, Russo MP, Puelo G, Marsan PA, Lorenzoni C, Marocco A, Recupero GR (1998) Construction of genetic maps for Citrus aurantium and C. latipes based on AFLP, RAPD and RFLP markers. Fruits 53:383–390

    Google Scholar 

  • Siviero A, Cristofani M, Machado M-A (2003) QTL mapping associated with rooting of stem cuttings from Citrus sunki x Poncirus trifoliata hybrids. Crop Breed Appl Biotech 3:83–88

    Google Scholar 

  • Soost RK, Cameron JW (1975) Citrus. In: Janick J, Moore JN (eds) Advances in fruit breeding. Purdue University, West Lafayette, Indiana, USA, pp 507–540

    Google Scholar 

  • Soost RK, Roose ML (1996) Citrus. In: Janick J, Moore JN (eds) Fruit breeding. Wiley, New York, USA, pp 257–323

    Google Scholar 

  • Stam P, Van Ooijen JW (1995) JoinMap (TM) version 2.0: software for the calculation of genetic linkage maps. CPRO-DLO, Wageningen

    Google Scholar 

  • Swingle WT, Reece PC (1967) The botany of citrus and its wild relatives. In: Reuther W, Webber HJ, Batchelor LD (eds) The Citrus Industry, Vol 1 (rev). Univ of California Press, Berkley, CA, USA, pp 190–430

    Google Scholar 

  • Thiel T, Michalek W, Varshney RK, Graner A (2003) Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theor Appl Genet 106:411–422

    PubMed  CAS  Google Scholar 

  • Torres AM, Mau-Lastovicka T, Williams TE, Soost RK (1985) Segregation distortion and linkage of citrus and Poncirus isozyme genes. J Hered 76:289–294

    CAS  Google Scholar 

  • Tozlu I, Guy CL, Moore GA (1999a) QTL analysis of Na+ and Cl− accumulation related traits in an intergeneric BC1 progeny of Citrus and Poncirus under saline and nonsaline environments. Genome 42:692–705

    Article  CAS  Google Scholar 

  • Tozlu I, Guy CL, Moore GA (1999b) QTL analysis of morphological traits in an intergeneric BC1 progeny of Citrus and Poncirus under saline and nonsaline environments. Genome 42:1020–1029

    Article  CAS  Google Scholar 

  • Van Ooijen JW, Voorrips RE (2001) JoinMap® 3.0, software for the calculation of genetic linkage maps. Plant Research International, Wageningen, The Netherlands

    Google Scholar 

  • Voorrips RE (2002) MapChart: software for the graphical presentation of linkage maps and QTLs. J Heredity 93:77–78

    Article  CAS  Google Scholar 

  • Weber CA, Moore GA, Deng Z, Gmitter FG Jr (2003) Mapping freeze tolerance quantitative trait loci in a Citrus grandis X Poncirus trifoliata F1 pseudo-testcross using molecular markers. J Am Soc Hortic Sci 128:508–514

    CAS  Google Scholar 

  • Yu J-K, La Rota EM, Kantety EV, Sorrells ME (2004) EST derived SSR markers for comparative mapping in wheat and rice. Mol Gen Genomics 271:742–751

    Article  CAS  Google Scholar 

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Acknowledgments

The authors would like to thank Mrs. Margie Wendell and Misty Holt for their excellent technical support. This research was supported in part under Project Number 0110-03I of the Florida Citrus Production Research Advisory Council, Peter McClure, Chairman, and 5200-125 from the California Citrus Research Board.

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Authors and Affiliations

  1. University of Florida, Citrus Research and Education Center, 700 Experiment Station Road, Lake Alfred, FL, 33850, USA

    Chunxian Chen, Young A Choi, Madhugiri Nageswara Rao, Shu Huang, Jaya R. Soneji & Fred G. Gmitter Jr.

  2. USDA-ARS, USHRL, 2001 South Rock Road, Ft. Pierce, FL, 34945, USA

    Kim D. Bowman, Phat M. Dang & T. Greg McCollum

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  1. Chunxian Chen
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  2. Kim D. Bowman
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  3. Young A Choi
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  5. Madhugiri Nageswara Rao
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  6. Shu Huang
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  9. Fred G. Gmitter Jr.
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Correspondence to Fred G. Gmitter Jr..

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Communicated by A. Abbott

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Table 7

Supplementary material one For CHEN’s Manuscript of EST-SSR Maps (PDF 267 kb)

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Chen, C., Bowman, K.D., Choi, Y.A. et al. EST-SSR genetic maps for Citrus sinensis and Poncirus trifoliata . Tree Genetics & Genomes 4, 1–10 (2008). https://doi.org/10.1007/s11295-007-0083-3

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  • DOI: https://doi.org/10.1007/s11295-007-0083-3

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