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Genomics of Citrus, a Major Fruit Crop of Tropical and Subtropical Regions

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Book cover Genomics of Tropical Crop Plants

Part of the book series: Plant Genetics and Genomics: Crops and Models ((PGG,volume 1))

Abstract

Genomics in citrus and closely related genera is relatively advanced, with many linkage maps, several bacterial artificial chromosome libraries, a physical map, a fairly large and well-annotated expressed sequence tag collection, several microarrays, and a low coverage (1.2x) genome sequence for sweet orange. This chapter reviews the various genomics resources available for citrus. Integration of these resources, particularly those developed in different laboratories, remains a challenge.

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References

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

    CAS  Google Scholar 

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

    Google Scholar 

  • Asins MJ, Bernet GP, Ruiz C, Cambra M, Guerri J, et al. (2004) QTL analysis of citrus tristeza virus-citradia interaction. Theor Appl Genet 108:603–611

    Article  PubMed  CAS  Google Scholar 

  • Ballester A, Cervera M, Pena, L (2007) Efficient production of transgenic citrus plants using isopentenyl transferase positive selection and removal of the marker gene by site-specific recombination. Plant Cell Rep 26:39–45

    Article  PubMed  CAS  Google Scholar 

  • Barkley NA, Roose ML, Krueger RR, Federici, CT (2006) Assessing genetic diversity and population structure in a citrus germplasm collection utilizing simple sequence repeat markers (SSRs). Theor Appl Genet 112:1519–1531

    Article  PubMed  CAS  Google Scholar 

  • Bausher MG, Singh ND, Lee S, Jansen RK, Daniell H (2006) The complete chloroplast genome sequence of Citrus sinensis (L.) Osbeck var ’Ridge Pineapple’: organization and phylogenetic relationships to other angiosperms. BMC Plant Biol 6:21

    Article  PubMed  CAS  Google Scholar 

  • Bond JE, Roose ML (1998) Agrobacterium-mediated transformation of the commercially important citrus cultivar Washington navel orange. Plant Cell Rep 18:229–234

    Article  CAS  Google Scholar 

  • Bretó MO, Ruiz C, Pina JA, Asins MJ (2001) The diversification of Citrus clementina Hort. Ex Tan., a vegetatively propagated crop species. Mol Phylogenet Evol 21:285–293

    Article  PubMed  CAS  Google Scholar 

  • Cercós M, Soler G, Iglesias DJ, Gadea J, Forment J, et al. (2006) Global analysis of gene expression during development and ripening of citrus fruit flesh. A proposed mechanism for citric acid utilization. Plant Mol Biol 62:513–527

    Article  PubMed  CAS  Google Scholar 

  • Cervera M, Pina JA, Juarez J, Navarro L, Pena, L (1998) Agrobacterium-mediated transformation of citrange: Factors affecting transformation and regeneration. Plant Cell Rep 18:271–278

    Article  CAS  Google Scholar 

  • Cervera M, Juarez J, Navarro L, Pena L (2005) Genetic transformation of mature citrus plants, In: Pena, L (ed.), Methods in Molecular Biology, Humana Press, pp. 177–187

    Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Chen C, Bowman KD, Choi YA, Dang PM, Rao MN, et al. (2007a) EST-SSR genetic maps for Citrus sinensis and Poncirus trifoliata. Tree Genetics and Genomes DOI 10.1007/s11295-007-0083-3

    Google Scholar 

  • Chen C, Zheng Q, Xiang X, Soneji JR, Huang S, et al. (2007b) Development of pGreen-derived GFP binary vectors for citrus transformation. HortSci 42:7–10

    CAS  Google Scholar 

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

    Google Scholar 

  • Close TJ, Wanamaker S, Lyon M, Mei G, Davies C, et al. (2006) A GeneChip®for Citrus. Plant & Animal Genomes Conf 14:W82, pg 26

    Google Scholar 

  • 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 Hort Sci 130:191–195

    CAS  Google Scholar 

  • de Araujo EF, de Queiroz LP, Machado MA (2003) What is Citrus? Taxonomic implications from a study of cp-DNA evolution in the tribe Citreae (Rutaceae subfamily Aurantioidaeae). Org Divers Evol 3:55–62

    Article  Google Scholar 

  • de Oliveira RP, Cristofani M, Machado MA (2005) Integrated genetic map of citrus based on RAPD markers. Fruits 60:187–193

    Article  CAS  Google Scholar 

  • Deng Z, Huang S, Ling P, Yu C, Tao Q, et al. (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 

  • Duan YX, Guo WW, Meng HJ, Tao NG, Li DD, et al. (2007) High efficient transgenic plant regeneration from embryogenic calluses of Citrus sinensis. Biologia Plantarum (Prague) 51:212–216

    Article  CAS  Google Scholar 

  • Durham RE, Liou PC, Gmitter FG Jr, 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, Roose ML (1997) Identification of closely related citrus cultivars with inter-simple sequence repeat markers. Theor Appl Genet 95:408–417

    Article  CAS  Google Scholar 

  • Fang DQ, Federici CT, Roose ML (1998a) Development of molecular markers linked to a gene controlling fruit acidity in Citrus. Genome 40:841–849

    Google Scholar 

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

    CAS  Google Scholar 

  • Federici CT, Fang DQ, Scora RW, Roose ML (1998) Phylogenetic relationships within the genus Citrus (Rutaceae) and related genera as revealed by RFLP and RAPD analysis. Theor Appl Genet 96:812–822

    Article  CAS  Google Scholar 

  • Forment J, Gadea J, Huerta L, Abizanda L, Agusti J, et al. (2005) Development of a citrus genome-wide EST collection and cDNA microarray as resources for genomic studies. Plant Mol Biol 57:375–391

    Article  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 

  • Gmitter FG Jr (1995) Origin, evolution and breeding of the grapefruit. Plant Breeding Rev 13:345–363

    Google Scholar 

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

    Article  CAS  Google Scholar 

  • Guerra M (1993) Cytogenetics of Rutaceae. V. High chromosomal variability in Citrus species revealed by CMA/DAPI staining. Heredity 71:234–241

    Google Scholar 

  • Gulsen O, Roose ML (2001) Lemons: diversity and relationships with selected Citrus genotypes as measured with nuclear genome markers. J Am Soc Hort Sci 126:309–317

    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 App Genet 84:49–56

    Article  CAS  Google Scholar 

  • Jayaprakasha GK, Patil BS (2007) In vitro evaluation of the antioxidant activities in fruit extracts from citron and blood orange. Food Chemistry 101:410–418

    Article  CAS  Google Scholar 

  • Kepiro J (2004) Molecular genetic analysis of nucellar embryony (apomixis) in Citrus maxima x Poncirus trifoliata. pp. 220. Ph.D. Dissertation, University of California, Riverside

    Google Scholar 

  • Ling P, Duncan LW, Deng Z, Dunn D, Hu X, et al. (2000) Inheritance of citrus nematode resistance and its linkage with molecular markers. Theor Appl Genet 100:1010–1017

    Article  CAS  Google Scholar 

  • Luro F, Lorieux M, Laigret F, Bové JM and Ollitraut P (1995) Cartographie du génome des agrumes á láide des marquers moléculaires et distorsions de ségrégation. In: INRA (ed.) Techniques et Utilisations des Marqueurs Moléculaires. INRA, Paris, pp. 69–82

    Google Scholar 

  • Matsuyama T, Akihama T, Ito Y, Omura M, Fukui K (1996) Characterization of heterochromatic regions in ‘Trovita’ orange (Citrus sinensis Osbeck) chromosomes by the fluorescent staining and FISH methods. Genome 39:941–945

    Article  PubMed  CAS  Google Scholar 

  • Mestre PF, Asins MJ, Pina JA, Carbonell EA, Navarro L (1997) Molecular markers flanking citrus tristeza virus resistance gene from Poncirus trifoliata (L.) Raf. Theor Appl Genet 94:458–464

    Article  CAS  Google Scholar 

  • Mirkov TE, Yang Z, Rai M, Molina JJ, Roose ML, et al. (in press) Toward positional cloning of the Citrus tristeza virus resistance gene. In: Karasev, AV and Hilf, ME (ed.), Citrus tristeza Virus Complex and Tristeza Diseases, APS Press

    Google Scholar 

  • Moore G (2001) Oranges and lemons: clues to the taxonomy of Citrus from molecular markers. Trends Genet 17:536–540

    Article  PubMed  CAS  Google Scholar 

  • Moraes A, Soares Filho WS, Guerra M (2007) Karyotype diversity and the origin of grapefruit. Chromosome Res 15:115–121

    Article  PubMed  CAS  Google Scholar 

  • Mozoruk J, Hunnicutt LE, Cave RD, Hunter WB, Bausher MG (2006) Profiling transcriptional changes in Citrus sinensis (L.) Osbeck challenged by herbivory from the xylem-feeding leafhopper Homalodisca coagulata (Say) by cDNA macroarray analysis Plant Sci 170:1068–1080

    CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  • Nicolosi E, La Malfa S, El-Otmani M, Neqbi M, Goldschmidt EE (2005) The search for the authentic citron (Citrus medica L.): Historic and genetic analysis. HortSci 40:1963–1968

    Google Scholar 

  • Pang X-M, Hu C-G, Deng, X-X (2007) Phylogenetic relationships within Citrus and its related genera as inferred from AFLP markers. Genet Resources Crop Evol 54:429–436

    Article  CAS  Google Scholar 

  • Pedrosa A, Schweizer D, Guerra M (2000) Cytological heterozygosity and the hybrid origin of sweet orange Citrus sinensis (L.) Osbeck. Theor Appl Genet 100:361–367

    Article  Google Scholar 

  • Pillitteri LJ, Lovatt CJ, Walling LL (2004) Isolation and characterization of a TERMINAL FLOWER homolog and its correlation with juvenility in Citrus. Plant Physiol 135:1540–1551

    Article  PubMed  CAS  Google Scholar 

  • Recupero GR, Russo MP, De Simone M, Natoli A, Marsan PA, Marocco A (2000) Development of molecular marker maps for rootstock breeding in Citrus. Acta Hort. 535:33–36

    CAS  Google Scholar 

  • Rico-Cabanas L, Martínez-Izquierdo JA (2007) CIRE1, a novel transcriptionally active Ty1-copia retrotransposon from Citrus sinensis. Mol Genet Genomics 277:365–377

    Article  PubMed  CAS  Google Scholar 

  • Roose ML, Schwarzacher T, Heslop-Harrison JS (1998) The chromosomes of Citrus and Poncirus species and hybrids: identification of characteristic chromosomes and physical mapping of rDNA loci using in situ hybridization and fluorochrome banding. J Hered 89:83–86

    Article  PubMed  CAS  Google Scholar 

  • Roose ML, Fang D, Cheng FS, Tayyar RA, Federici CT, et al. (2000) Mapping the Citrus genome. Acta Horticulturae 535:25–32

    CAS  Google Scholar 

  • 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 

  • Shimada T, Fuiii H, Endo T, Yazaki J, Kishimoto N, et al. (2005) Toward comprehensive expression profiling by microarray analysis in citrus: monitoring the expression profiles of 2213 genes during fruit development. Plant Sci 168:1383–1385

    Article  CAS  Google Scholar 

  • Terol J, Conesa A, Colmenero JM, Cercos M, Tadeo FR, et al. (2007) Analyses of 13000 unique Citrus clusters associated with fruit quality, production and salinity tolerance. BMC Genomics 8:31

    Article  PubMed  CAS  Google Scholar 

  • Torres AM, Soost RK, Diedenhofen U (1978) Leaf isozymes as genetic markers in Citrus. Am J Bot 65:869–881

    Article  Google Scholar 

  • Tozlu I, Guy CL, Moore GA (1999a) 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 

  • Tozlu I, Guy CL, Moore GA (1999b) 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 

  • Yamamoto M, Tominaga S (2003) High chromosomal variability of mandarins (Citrus spp.) revealed by CMA banding. Euphytica 129:267–274

    Article  CAS  Google Scholar 

  • Yang ZN, Ingelbrecht I, Louzada E, Skaria M, Mirkov, TE (2000) Agrobacterium mediated transformation of the commercially important grapefruit cultivar Rio Red. Plant Cell Rep 19:1203–1211

    Article  CAS  Google Scholar 

  • Yang ZN, Ye XR, Choi S, Molina J, Moonan F, et al. (2001) Construction of a 1.2 Mb contig including the Citrus tristeza virus resistance gene locus using a bacterial artificial chromosome library of Poncirus trifoliata. Genome 44:382–393

    Article  PubMed  CAS  Google Scholar 

  • Yang ZN, Ye XR, Molina J, Roose ML, Mirkov, TE (2003) Sequence analysis of a 282-kb region surrounding the Citrus tristeza virus resistance gene (Ctv) locus in Poncirus trifoliata. Plant Physiol 131:482–492

    Article  PubMed  CAS  Google Scholar 

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Author information

Authors and Affiliations

  1. Department of Botany & Plant Sciences, University of California, Riverside, CA 92521, U.S.A.

    Mikeal L. Roose

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  1. Mikeal L. Roose
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  2. Timothy J. Close
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Editor information

Editors and Affiliations

  1. USDA-ARS, PBARC Hawaii Agriculture Research Center, 99-193 Aiea Heights Drive, Aiea 96701

    Paul H. Moore

  2. Department of Plant Biology, University of lllinois at Urbana-Champaign, 1201 W. Gregory Drive Urbana 61801 288 ERML, MC-051, Champaign, IL, USA

    Ray Ming

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Roose, M.L., Close, T.J. (2008). Genomics of Citrus, a Major Fruit Crop of Tropical and Subtropical Regions. In: Moore, P.H., Ming, R. (eds) Genomics of Tropical Crop Plants. Plant Genetics and Genomics: Crops and Models, vol 1. Springer, New York, NY. https://doi.org/10.1007/978-0-387-71219-2_8

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