Skip to main content
SpringerLink
Log in

Molecular Markers in Papayas

  • Chapter
  • First Online:
Book cover Genetics and Genomics of Papaya

Part of the book series: Plant Genetics and Genomics: Crops and Models ((PGG,volume 10))

Abstract

Molecular markers have been applied to papaya crop improvement for two decades. They were initially used to study the genetic diversity among the Caricaceae, containing the cultivated Carica papaya and 21 related wild species. Originally, these were all placed within the genus Carica. However, in 2000, molecular markers were employed to show that several members of this genus were genetically distant from C. papaya, and they were subsequently placed in a new genus Vasconcellea. C. papaya plants exhibit three potential sex types, and the ability to identify sex of a plant at an early growth stage would greatly benefit commercial producers in terms of planting management. Therefore, much marker research has been applied to the identification of DNA markers for the differentiation and selection of male, female, and hermaphrodite plants. Papaya is an ideal model tropical fruit species for genomic studies. It has a relatively small genome size of 372 Mb, is diploid 2n = 18, produces climacteric fruit, and has a short generation time. The papaya genome was recently sequenced and several genetic and physical maps exist. These have been developed specifically to identify DNA-based markers for assisted selection of important traits such as resistance to papaya ringspot virus and flesh color. Although a substantial quantity of data on papaya genomics has been produced, this is often trait or genome specific and not always widely applicable due to problems associated with irreproducibility and non-transferability. Future papaya genomics efforts must be focused on the identification of functional genetic components that control the traits of interest. Tools based on the expressed genome sequences that are closely associated with significant trait loci will become the highly efficient and transferable markers of the future for enhanced papaya breeding objectives.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Aradhya MK, Manshardt RM, Zee F, Morden CW (1999) A phylogenetic analysis of the genus Carica L. (Caricaceae) based on restriction fragment length variation in a cpDNA intergenic spacer region. Genet Resour Crop Evol 46(6):579–586

    Article  Google Scholar 

  • Arumuganathan K, Earle E (1991) Nuclear DNA content of some important plant species. Plant Mol Biol Rep 9(3):208–218

    Article  CAS  Google Scholar 

  • Badillo VM (2000) Carica L. vs. Vasconcella St. Hil. (Caricaceae): con la rehabilitacion de este ultimo. Ernstia 10:74–79

    Google Scholar 

  • Blas AL, Yu Q, Chen C, Veatch O, Moore PH, Paull RE, Ming R (2009) Enrichment of a papaya high-density genetic map with AFLP markers. Genome Res 52(8):716–725

    Article  CAS  Google Scholar 

  • Blas AL, Ming R, Liu Z, Veatch OJ, Paull RE, Moore PH, Yu Q (2010) Cloning of the papaya chromoplast-specific lycopene β-cyclase, CpCYC-b, controlling fruit flesh color reveals conserved microsynteny and a recombination hot spot1[W][OA]. Plant Physiol 152(4):2013–2022

    Article  PubMed  CAS  Google Scholar 

  • Blas A, Yu Q, Veatch O, Paull R, Moore P, Ming R (2012) Genetic mapping of quantitative trait loci controlling fruit size and shape in papaya. Mol Breeding 29(2):457–466. doi:10.1007/s11032-011-9562-1

    Article  Google Scholar 

  • Chaves-Bedoya G, Nuñez V (2007) A SCAR marker for the sex types determination in Colombian genotypes of Carica papaya. Euphytica 153(1):215–220

    CAS  Google Scholar 

  • Chen C, Yu Q, Hou S, Li Y, Eustice M, Skelton RL, Veatch O, Herdes RE, Diebold L, Saw J, Feng Y, Qian W, Bynum L, Wang L, Moore PH, Paull RE, Alam M, Ming R (2007) Construction of a sequence-tagged high-density genetic map of papaya for comparative structural and evolutionary genomics in brassicales. Genetics 177(4):2481–2491

    Article  PubMed  CAS  Google Scholar 

  • Coppens G, d’Eeckenbrugge C, Drew R, Kyndt T, Scheldeman X (2013) Vasconcellea for papaya improvement. In: Ming R, Moore P (eds) Genetics and genomics of papaya. Springer Science + Business Media, New York

    Google Scholar 

  • de Oliveira EJ, Dantas JLL, Castellen MDS, de Lima DS, Barbosa HD, Motta TBN (2007) Molecular markers for sex identification in papaya. Pesquisa Agropecuaria Brasileira 42(12):1747–1754

    Article  Google Scholar 

  • de Oliveira EJ, Dantas JLL, Castellen MDS, Machado MD (2008) Identification of microsatellites for papaya by DNA data bank exploration. Revista Brasileira De Fruticultura 30(3):841–845

    Article  Google Scholar 

  • de Oliveira EJ, Amorim VBO, Matos ELS, Costa JL, Castellen MD, Padua JG, Dantas JLL (2010a) Polymorphism of microsatellite markers in papaya (Carica papaya L.). Plant Mol Biol Rep 28(3):519–530

    Article  Google Scholar 

  • de Oliveira EJ, dos Santos Silva A, de Carvalho FM, dos Santos LF, Costa JL, de Oliveira Amorim VB, Dantas JLL (2010b) Polymorphic microsatellite marker set for Carica papaya L. and its use in molecular-assisted selection. Euphytica 173(2):279–287

    Article  Google Scholar 

  • Deputy JC, Ming R, Ma H, Liu Z, Fitch MMM, Wang M, Manshardt R, Stiles JI (2002) Molecular markers for sex determination in papaya (Carica papaya L.). Theor Appl Genet 106(1):107–111

    PubMed  CAS  Google Scholar 

  • Dillon S, Ramage C, Drew R, Ashmore S (2005) Genetic mapping of a PRSV-P resistance gene in “highland papaya” based on inheritance of RAF markers. Euphytica 145(1):11–23

    Article  CAS  Google Scholar 

  • Dillon S, Ramage C, Ashmore S, Drew RA (2006) Development of a codominant CAPS marker linked to PRSV-P resistance in highland papaya. Theor Appl Genet 113(6):1159–1169

    Article  PubMed  CAS  Google Scholar 

  • Drew RA, O’Brien C, Magdalita PM (1998) Development of Carica interspecific hybrids. Acta Hortic 461:285–292

    Google Scholar 

  • Eustice M, Yu Q, Lai CW, Hou S, Thimmapuram J, Liu L, Alam M, Moore PH, Presting GG, Ming R (2008) Development and application of microsatellite markers for genomic analysis of papaya. Tree Genet Genome 4(2):333–341

    Article  Google Scholar 

  • Fan M-J, Chen S, Kung Y-J, Cheng Y-H, Bau H-J, Su T-T, Yeh S-D (2009) Transgene-specific and event-specific molecular markers for characterization of transgenic papaya lines resistant to papaya ringspot virus. Transgenic Res 18(6):971–986

    Article  PubMed  CAS  Google Scholar 

  • Fitch MMM, Manshardt RM, Gonsalves D, Slightom JL, Sanford JC (1990) Stable transformation of papaya via microprojectile bombardment. Plant Cell Rep 9(4):189–194

    Article  CAS  Google Scholar 

  • Gangopadhyay G, Roy SK, Ghose K, Poddar R, Bandyopadhyay T, Basu D, Mukherjee KK (2007) Sex detection of Carica papaya and Cycas circinalis in pre-flowering stage by ISSR and RAPD. Curr Sci 92(4):524–526

    CAS  Google Scholar 

  • Hofmeyr JDJ (1938) Genetical studies of Carica papaya L. I. The inheritance and relation of sex and certain plant characteristics. II. Sex reversal and sex forms. South African Department of Agriculture and Science Bulletin No 187

    Google Scholar 

  • Hofmeyr JDJ (1939) Sex-linked inheritance in Carica Papaya L. S Afr J Sci 36:283–285

    Google Scholar 

  • Jobin-Decor MP, Graham GC, Henry RJ, Drew RA (1997) RAPD and isozyme analysis of genetic relationships between Carica papaya and wild relatives. Genet Resour Crop Evol 44(5):471–477

    Article  Google Scholar 

  • Kim MS, Moore PH, Zee F, Fitch MMM, Steiger DL, Manshardt RM, Paull RE, Drew RA, Sekioka T, Ming R (2002) Genetic diversity of Carica papaya as revealed by AFLP markers. Genome Res 45(3):503–512

    Article  CAS  Google Scholar 

  • Lai CWJ, Yu Q, Hou S, Skelton RL, Jones MR, Lewis KLT, Murray J, Eustice M, Guan P, Agbayani R, Moore PH, Ming R, Presting GG (2006) Analysis of papaya BAC end sequences reveals first insights into the organization of a fruit tree genome. Mol Genet Genomics 276(1):1–12

    Article  PubMed  CAS  Google Scholar 

  • Lemos EGM, Silva CLSP, Zaidan HA (2002) Identification of sex in Carica papaya L. using RAPD markers. Euphytica 127(2):179–184

    Article  CAS  Google Scholar 

  • Ma H, Moore PH, Liu Z, Kim MS, Yu Q, Fitch MMM, Sekioka T, Paterson AH, Ming R (2004) High-density linkage mapping revealed suppression of recombination at the sex determination locus in papaya. Genetics 166(1):419–436

    Article  PubMed  CAS  Google Scholar 

  • Magdalita PM, Drew RA, Adkins SW, Godwin ID (1997) Morphological, molecular and cytological analyses of Carica papaya X C. cauliflora interspecific hybrids. Theor Appl Genet 95(1):224–229

    Article  CAS  Google Scholar 

  • Manshardt RM, Drew RA (1998) Biotechnology of papaya. Acta Hortic 461:65–74

    Google Scholar 

  • Ming R, Moore PH, Zee F, Abbey CA, Ma H, Paterson AH (2001) Construction and characterization of a papaya BAC library as a foundation for molecular dissection of a tree-fruit genome. Theor Appl Genet 102(6):892–899

    Article  CAS  Google Scholar 

  • Ming R, Yu Q, Moore PH (2007) Sex determination in papaya. Semin Cell Dev Biol 18(3):401–408

    Article  PubMed  CAS  Google Scholar 

  • Ming R, Hou S, Feng Y, Yu Q, Dionne-Laporte A, Saw JH, Senin P, Wang W, Ly BV, Lewis KLT, Salzberg SL, Feng L, Jones MR, Skelton RL, Murray JE, Chen C, Qian W, Shen J, Du P, Eustice M, Tong E, Tang H, Lyons E, Paull RE, Michael TP, Wall K, Rice DW, Albert H, Wang M-L, Zhu YJ, Schatz M, Nagarajan N, Acob RA, Guan P, Blas A, Wai CM, Ackerman CM, Ren Y, Liu C, Wang J, Wang J, Na J-K, Shakirov EV, Haas B, Thimmapuram J, Nelson D, Wang X, Bowers JE, Gschwend AR, Delcher AL, Singh R, Suzuki JY, Tripathi S, Neupane K, Wei H, Irikura B, Paidi M, Jiang N, Zhang W, Presting G, Windsor A, Navajas-Pérez R, Torres MJ, Feltus FA, Porter B, Li Y, Burroughs AM, Luo M-C, Liu L, Christopher DA, Mount SM, Moore PH, Sugimura T, Jiang J, Schuler MA, Friedman V, Mitchell-Olds T, Shippen DE, dePamphilis CW, Palmer JD, Freeling M, Paterson AH, Gonsalves D, Wang L, Alam M (2008) The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature 452(7190):991–996

    Article  PubMed  CAS  Google Scholar 

  • Moore GA, Litz RE (1984) Biochemical markers for Carica papaya, C. cauliflora, and plants from somatic embryos of their hybrid. J Am Soc Hortic Sci 109(2):213–218

    CAS  Google Scholar 

  • Nagarajan N, Navajas-Pérez R, Pop M, Alam M, Ming R, Paterson A, Salzberg S (2008) Genome-wide analysis of repetitive elements in papaya. Trop Plant Biol 1(3):191–201

    Article  CAS  Google Scholar 

  • Niroshini E, Everard J, Karunanayake EH, Tirimanne TLS (2008) Detection of sequence characterized amplified region (SCAR) markers linked to sex expression in Carica papaya L. J Natl Sci Found Sri Lanka 36(2):145–150

    CAS  Google Scholar 

  • Noorda-Nguyen K, Ruizong J, Ayumi A, Qingyi Y, Nishijima W, Yun JZ (2010) Identification of disease tolerance loci to Phytophthora palmivora in Carica papaya using molecular marker approach. Acta Hortic 851:189–196

    CAS  Google Scholar 

  • O’Brien CM, Drew RA (2009) Potential for using Vasconcellea parviflora as a bridging species in intergeneric hybridisation between V. pubescens and Carica papaya. Aust J Bot 57:592–601

    Article  Google Scholar 

  • O’Brien C, Drew RA (2010) Marker-assisted hybridisation and backcrossing between Vasconcellea species and Carica papaya for PRSV-P resistance. Acta Hortic 859:361–368

    Google Scholar 

  • Ocampo Pérez J, d’Eeckenbrugge C, Risterucci AM, Dambier D, Ollitrault P (2007) Papaya genetic diversity assessed with microsatellite markers in germplasm from the Caribbean region. Acta Hortic 740:93–101

    Google Scholar 

  • Oliveira EJ, Dantas JLL, Castellen MS, Machado MD (2008) Identificac ṃa ̃o de microssate ́lites para o mamoeiro por meio da explorac ṃa ̃o do banco de dados de DNA. Rev Bras Frutic 30:841–845

    Article  Google Scholar 

  • Parasnis AS, Ramakrishna W, Chowdari KV, Gupta VS, Ranjekar PK (1999) Microsatellite (GATA)n reveals sex-specific differences in papaya. Theor Appl Genet 99(6):1047–1052

    Article  CAS  Google Scholar 

  • Parasnis AS, Gupta VS, Tamhankar SA, Ranjekar PK (2000) A highly reliable sex diagnostic PCR assay for mass screening of papaya seedlings. Mol Breeding 6(3):337–344

    Article  CAS  Google Scholar 

  • Pérez JO, Dambier D, Ollitrault P, D'eeckenbrugge GC, Brottier P, Froelicher Y, Risterucci A-M (2006) Microsatellite markers in Carica papaya L.: isolation, characterization and transferability to Vasconcellea species. Mol Ecol Notes 6(1):212–217

    Article  Google Scholar 

  • Porter B, Zhu Y, Christopher D (2009a) Carica papaya genes regulated by Phytophthora palmivora: a model system for genomic studies of compatible Phytophthora-plant interactions. Trop Plant Biol 2(2):84–97

    Article  CAS  Google Scholar 

  • Porter BW, Paidi M, Ming R, Alam M, Nishijima WT, Zhu YJ (2009b) Genome-wide analysis of Carica papaya reveals a small NBS resistance gene family. Mol Genet Genomics 281(6):609–626

    Article  PubMed  CAS  Google Scholar 

  • Ratchadaporn J, Sureeporn K, Khumcha U (2007) An analysis on DNA fingerprints of thirty papaya cultivars (Carica papaya L.), grown in Thailand with the use of amplified fragment length polymorphisms technique. Pak J Biol Sci 10(18):3072

    Article  PubMed  CAS  Google Scholar 

  • Santos SC, Ruggiero C, Silva CLSP, Lemos EGM (2003) A microsatellite library for Carica papaya L. cv. Sunrise solo. Revista Brasileira De Fruticultura 25(2):263–267

    Article  Google Scholar 

  • Sharon D, Hillel J, Vainstein A, Lavi U (1992) Application of DNA fingerprints for identification and genetic analysis of Carica papaya and other Carica species. Euphytica 62(2):119–126

    Article  CAS  Google Scholar 

  • Somsri S, Bussabakornkul S (2008) Identification of certain papaya cultivars and sex identification in papaya by DNA Amplification Fingerprinting (DAF). Acta Hortic 787:197–206

    CAS  Google Scholar 

  • Somsri S, Fletcher RJ, Jobin M, Drew R, Lawson W, Graham MW (1998) Developing molecular markers for sex prediction in papaya (Carica papaya L.). Acta Hortic 461:141–148

    CAS  Google Scholar 

  • Sondur SN, Manshardt RM, Stiles JI (1996) A genetic linkage map of papaya based on randomly amplified polymorphic DNA markers. Theor Appl Genet 93(4):547–553

    Article  CAS  Google Scholar 

  • Stiles JI, Lemme C, Sondur S, Morshidi MB, Manshardt R (1993) Using randomly amplified polymorphic DNA for evaluating genetic relationships among papaya cultivars. Theor Appl Genet 85(6):697–701

    CAS  Google Scholar 

  • Storey WB (1938) Segregation of sex types in Solo papaya and their application to the selection of seed. Am Soc Hortic Sci Proc 35:83–85

    Google Scholar 

  • Tan SC, Weinheimer EA (1976) The isoenzyme patterns of developing fruit and mature leaf of papaya (Carica papaya L.). Sains Malays J Nat Sci 5(1):7–14

    Google Scholar 

  • Tennant PF, Gonsalves C, Ling KS, Fitch MMM, Manshardt RM, Slightom JL, Gonsalves D (1994) Differential protection against Papaya Ringspot Virus isolates in coat protein gene transgenic papaya and classically cross protected papaya. Phytopathology 1359–1366

    Google Scholar 

  • Urasaki N, Tarora K, Uehara T, Chinen I, Terauchi R, Tokumoto M (2002a) Rapid and highly reliable sex diagnostic PCR assay for papaya (Carica papaya L.). Breeding Sci 52(4):333–335

    Article  CAS  Google Scholar 

  • Urasaki N, Tokumoto M, Tarora K, Ban Y, Kayano T, Tanaka H, Oku H, Chinen I, Terauchi R (2002b) A male and hermaphrodite specific RAPD marker for papaya (Carica papaya L.). Theor Appl Genet 104(2):281–285

    Article  PubMed  CAS  Google Scholar 

  • Van Droogenbroeck B, Breyne P, Goetghebeur P, Romeijn-Peeters E, Kyndt T, Gheysen G (2002) AFLP analysis of genetic relationships among papaya and its wild relatives (Caricaceae) from Ecuador. Theor Appl Genet 105(2):289–297

    Article  PubMed  Google Scholar 

  • Wai C, Ming R, Moore P, Paull R, Yu Q (2010) Development of chromosome-specific cytogenetic markers and merging of linkage fragments in papaya. Trop Plant Biol 3(3):171–181

    Article  Google Scholar 

  • Wang J, Chen C, Na J-K, Yu Q, Hou S, Paull RE, Moore PH, Alam M, Ming R (2008) Genome-wide comparative analyses of microsatellites in papaya. Trop Plant Biol 1(3):278–292

    Article  CAS  Google Scholar 

  • Yamamoto H (1964) Comparison of the carotenoids in yellow- and red-fleshed Carica papaya. Nature 201:1049–1050

    Article  PubMed  CAS  Google Scholar 

  • Yu Q, Tong E, Skelton RL, Bowers JE, Jones MR, Murray JE, Hou S, Guan P, Acob RA, Luo M-C, Moore PH, Alam M, Paterson AH, Ming R (2009) A physical map of the papaya genome with integrated genetic map and genome sequence. BMC Genomics 10(1):371

    Article  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. School of Biomolecular and Physical Sciences, Griffith University, 170 Kessels Road, Nathan, QLD, 4111, Australia

    Chutchamas Kanchana-udomkan & Rod Drew

  2. Department of Agriculture and Food Systems, Melbourne School of Land and Environment, Melbourne, VIC, 3010, Australia

    Rebecca Ford

Authors
  1. Chutchamas Kanchana-udomkan
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Rebecca Ford
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Rod Drew
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Rod Drew .

Editor information

Editors and Affiliations

  1. Department of Plant Biology, University of Illinois at Urbana-Champai, Urbana, Illinois, USA

    Ray Ming

  2. Hawaii Agriculture Research Center, Kaneohe, Hawaii, USA

    Paul H. Moore

Rights and permissions

Reprints and permissions

Copyright information

© 2014 Springer Science+Business Media New York

About this chapter

Cite this chapter

Kanchana-udomkan, C., Ford, R., Drew, R. (2014). Molecular Markers in Papayas. In: Ming, R., Moore, P. (eds) Genetics and Genomics of Papaya. Plant Genetics and Genomics: Crops and Models, vol 10. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-8087-7_19

Download citation

Publish with us

Policies and ethics

Search

Navigation