Molecular Genetic Mapping of Papaya

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


The development of high-density genetic maps is a major advancement in papaya genomic research. Two low-density genetic maps were developed using morphological markers and randomly amplified polymorphic DNA (RAPD) markers. Amplified fragment length polymorphism (AFLP) markers and simple sequence repeat (SSR) markers were used to develop three high-density genetic maps. Detailed analysis of the genetic maps provides insights into the nature of papaya chromosomes including the location of the sex determination region of the sex chromosomes, recombination hot spots, methylation patterns, centromere locations, and regions of high sequence divergence. The high-density SSR genetic map was integrated with the physical map, whole genome sequence, and cytological data, enhancing our ability to identify agronomic important genes.


Linkage Group Amplify Fragment Length Polymorphism Simple Sequence Repeat Marker Amplify Fragment Length Polymorphism Marker Restriction Fragment Length Polymorphism 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


  1. Alonso-Blanco C, Peeters AJM, Koornneef M, Lister C, Dean C et al (1998) Development of an AFLP based linkage map of Ler, Col and Cvi Arabidopsis thaliana ecotypes and construction of a Ler/Cvi recombinant inbred line population. Plant J 14:259–271PubMedCrossRefGoogle Scholar
  2. Arumuganathan K, Earle ED (1991) Nuclear DNA content of some important plant species. Plant Mol Biol Rep 93:208–219CrossRefGoogle Scholar
  3. Becerra Lopez-Lavalle LA, Matheson B, Brubaker CL (2011) A genetic map of an Australian wild Gossypium C genome and assignment of homoeologies with tetraploid cultivated cotton. Genome 54(9):779–794PubMedCrossRefGoogle Scholar
  4. Bert PF, Charme G, Sourdille P, Hayward MD (1999) A high-density molecular map for ryegrass (Lolium perenne). Theor Appl Genet 99:445–452PubMedCrossRefGoogle Scholar
  5. Blas AL, Yu Q, Che C, Veatch O, Moore PH, Paull RE, Ming R (2009) Enrichment of a papaya high-density genetic map with AFLP markers. Genome 52:716–725PubMedCrossRefGoogle Scholar
  6. Boyko E, Kalendar R, Korzun V, Fellers J, Korol A et al (2002) A high-density cytogenetic map of the Aegilops tauschii genome incorporating retrotransposons and defense-related genes: insights into cereal chromosome structure and function. Plant Mol Biol 48:767–790PubMedCrossRefGoogle Scholar
  7. Castiglioni P, Ajmone-Marsan P, van Wijk R, Motto M (1999) AFLP markers in a molecular linkage map of maize: codominant scoring and linkage group distribution. Theor Appl Genet 99(3–4):425–431PubMedCrossRefGoogle Scholar
  8. Chao S, Sharp PJ, Worland AJ, Warham EJ, Koebner RMD et al (1989) RFLP-based genetic maps of wheat homoeologous group 7 chromosomes. Theor Appl Genet 78:495–504CrossRefGoogle Scholar
  9. Chen C, Yu Q, Hou S, Li Y, Eustice M et al (2007) Construction of a sequence-tagged high-density genetic map of papaya for comparative structural and evolutionary genomics in Brassicales. Genetics 177(4):2481–2491PubMedCrossRefGoogle Scholar
  10. Copenhaver GP, Nickel K, Kuromori T, Benito MI, Kaul S et al (1999) Genetic definition and sequence analysis of Arabidopsis centromeres. Science 286:2468–2474PubMedCrossRefGoogle Scholar
  11. Davis GL, McMullen MD, Baysdorfer C, Musket T, Grant D et al (1999) A maize map standard with sequenced core markers, grass genome reference points and 932 expressed sequence tagged sites (ESTs) in a 1736-locus map. Genetics 152:1137–1172PubMedGoogle Scholar
  12. Deputy JC, Ming R, Ma H, Liu Z, Fitch MMM et al (2002) Molecular markers for sex determination in papaya (Carica papaya L.). Theor Appl Genet 106:107–111PubMedGoogle Scholar
  13. Draye X, Lin YR, Qian XY, Bowers JE, Burow GB et al (2001) Toward integration of comparative genetic, physical, diversity, and cytomolecular maps for grasses and grains, using the sorghum genome as a foundation. Plant Physiol 125:1325–1341PubMedCrossRefGoogle Scholar
  14. Fitch MMM, Manshardt RM, Gonsalves D, Slightom JL (1992) Virus resistant papaya derived from tissue bombarded with the coat protein gene of the papaya ringspot virus. Nat Biotechnol 10:1466–1472CrossRefGoogle Scholar
  15. Grodzieker T, Williams J, Sharp P, Sambrook J (1974) Physical mapping of temperature sensitive mutations of adenovirus. Cold Spring Harb Symp Quant Biol 39:439–446CrossRefGoogle Scholar
  16. Haanstra J, Wye C, Verbakel H, Meijer-Dekens F, van den Berg P et al (1999) An integrated high-density RFLP-AFLP map of tomato based on two Lycopersicon esculentum × L. pennellii F2 populations. Theor Appl Genet 99:254–271CrossRefGoogle Scholar
  17. Harushima Y, Yano M, Shomura A, Sato M, Shimano T et al (1998) A high-density rice genetic linkage map with 2275 markers using a single F2 population. Genetics 148:479–494PubMedGoogle Scholar
  18. Hofmeyr JDJ (1938) Genetical studies of Carica papaya L. South Afr J Sci 35:300–304Google Scholar
  19. Hofmeyr JDJ (1939) Sex-linked inheritance in Carica papaya L. South Afr J Sci 36:283–285Google Scholar
  20. Hofmeyr JDJ (1967) Some genetic breeding aspects of Carica papaya L. Agron Trop 17:345–351Google Scholar
  21. Keim P, Schupp JM, Travis SE, Clayton K, Zhu T et al (1997) A high-density soybean genetic map based on AFLP markers. Crop Sci 37:537–543CrossRefGoogle Scholar
  22. Klein PE, Klein RR, Cartinhour SW, Ulanch PE, Dong J et al (2000) A high-throughput AFLP-based method for constructing integrated genetic and physical maps: progress toward a sorghum genome map. Genome Res 10:789–807PubMedCrossRefGoogle Scholar
  23. Liu Z, Moore PH, Ma H, Ackerman CM, Ragiba M et al (2004) A primitive Y chromosome in papaya marks incipient sex chromosome evolution. Nature 427:348–352PubMedCrossRefGoogle Scholar
  24. Lombard V, Delourme R (2001) A consensus linkage map for rapeseed (Brassica napus L.): construction and integration of three individual maps from DH populations. Theor Appl Genet 103:491–507CrossRefGoogle Scholar
  25. Ma H, Moore PH, Liu Z, Kim MS, Yu Q et al (2004) High-density linkage mapping revealed suppression of recombination at the sex determination locus in papaya. Genetics 166:419–436PubMedCrossRefGoogle Scholar
  26. Martin G, Brommonschenkel SH, Chunwongse J, Frary A, Ganal M et al (1993) Map-based cloning of a protein kinase gene conferring disease resistance in tomato. Science 26(2):1432–11436CrossRefGoogle Scholar
  27. Mignouna HD, Mank RA, Ellis N, Van Den Bosch N, Asiedu R et al (2002) A genetic linkage map of water yam (Dioscorea alata L.) based on AFLP markers and QTL analysis for anthracnose resistance. Theor Appl Genet 105:726–735PubMedCrossRefGoogle Scholar
  28. 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 102:892–899CrossRefGoogle Scholar
  29. Ming R, Hou S, Feng Y, Yu Q, Dionne-Laporte A et al (2008) The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature 452:991–996PubMedCrossRefGoogle Scholar
  30. Morgante M, Olivieri AM (1993) PCR-amplified microsatellites as markers in plant genetics. Plant J 1:175–182CrossRefGoogle Scholar
  31. Parasni AS, Gupta VS, Tamhankar SA, Ranjekar PK (2000) A highly reliable sex diagnostic PCR assay for mass screening of papaya seedlings. Mol Breed 6:337–344CrossRefGoogle Scholar
  32. Paterson A, Bowers JE, Burow MD, Draye X, Elsik CG et al (2000) Comparative genomics of plant chromosomes. Plant Cell 12:1523–1539PubMedGoogle Scholar
  33. Peng J, Korol AB, Fahim T, Roder MS, Ronin YI, Li YC, Nevo E (2000) Molecular genetic maps in wild emmer wheat, Triticum dicoccoides: genome-wide coverage, massive negative interference, and putative quasi-linkage. Genome Res 10(10):1509–1531PubMedCrossRefGoogle Scholar
  34. Peters JL, Constandt H, Neyt P, Cnops G, Zethof J et al (2001) A physical amplified fragment-length polymorphism map of Arabidopsis. Plant Physiol 127:1579–1589PubMedCrossRefGoogle Scholar
  35. Risterucci AM, Grivet L, N’Goran JAK, Pieretti I, Flament MH, Lanaud C (2000) A high-density linkage map of Theobroma cacao L. Theor Appl Genet 101:948–955CrossRefGoogle Scholar
  36. Sondur SN, Manshardt RM, Stiles JI (1995) Genetics of growth rate and flowering time in papaya (Carica papaya L.). J Quant Trait Loci.
  37. Sondur SN, Manshardt RM, Stiles JI (1996) A genetic linkage map of papaya based on randomly amplified polymorphic DNA markers. Theor Appl Genet 93:547–553CrossRefGoogle Scholar
  38. 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 85:697–701Google Scholar
  39. Storey WB (1953) Genetics of papaya. J Hered 44:70–78Google Scholar
  40. Tanksley SD, Ganal MW, Prince JP, de Vicente MC, Bonierbale MW et al (1992) High density molecular linkage maps of the tomato and potato genomes. Genetics 132:1141–1160PubMedGoogle Scholar
  41. Tanksley SD, Ganal MW, Martin GB (1995) Chromosome landing: a paradigm for map-based gene cloning in plants with large genomes. Trends Genet 11:63–68PubMedCrossRefGoogle Scholar
  42. Urasaki N, Tokumoto M, Tarora K, Ban Y, Kayano T et al (2002) A male and hermaphrodite specific RAPD marker for papaya (Carica papaya L). Theor Appl Genet 104:281–285PubMedCrossRefGoogle Scholar
  43. Verde I, Lauria M, Dettori MT, Vendramin E, Balconi C, Micali S et al (2005) Microsatellite and AFLP markers in the Prunus persica [L. (Batsch)] P. ferganensis BC1 linkage map: saturation and coverage improvement. Theor Appl Genet 111(6):1013–1021PubMedCrossRefGoogle Scholar
  44. Vos P, Hogers R, Bleeker M, Reijans M, van de Lee T et al (1995) AFLP: a new tool for DNA fingerprinting. Nucleic Acids Res 23:4407–4414PubMedCrossRefGoogle Scholar
  45. Vuylsteke M, Mank R, Antonise R, Bastiaans E, Senior ML et al (1999) Two high-density AFLP linkage maps of Zea mays L.: analysis of distribution of AFLP markers. Theor Appl Genet 99:921–935CrossRefGoogle Scholar
  46. Wai CM, Ming R, Moore PH, Paull RE, Yu Q (2010) Development of chromosome-specific cytogenetic markers and merging of linkage fragments in papaya. Trop Plant Biol 3:171–181CrossRefGoogle Scholar
  47. Wikstrom N, Savolainen V, Chase MW (2001) Evolution of the angiosperms: calibrating the family tree. Proc Biol Sci 268:2211–2220PubMedCrossRefGoogle Scholar
  48. Williams JGK, Kubelik AR, Livak KJ, Rafalski JA, Tingey SV (1990) DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res 18:6531–6653PubMedCrossRefGoogle Scholar
  49. Yu Q, Hou S, Hobza R, Feltus FA, Wang X et al (2007) Chromosomal location and gene paucity of the male specific region on papaya Y chromosome. Mol Genet Genomics 278:177–185PubMedCrossRefGoogle Scholar
  50. Yu Q, Hou S, Feltus FA, Jones MR, Murray JE, Veatch O et al (2008) Low X/Y divergence in four pairs of papaya sex-linked genes. Plant J 53(1):124–132PubMedCrossRefGoogle Scholar
  51. Yu Q, Tong E, Skelton RL, Bowers JE, Jones MR et al (2009) A physical map of the papaya genome with integrated genetic map and genome sequence. BMC Genomics 10:371PubMedCrossRefGoogle Scholar
  52. Zhang W, Wang X, Yu Q, Ming R, Jiang J (2008) DNA methylation and heterochromatinization in the male-specific region of the primitive Y chromosome of papaya. Genome Res 18:1938–1943PubMedCrossRefGoogle Scholar
  53. Zhang W, Wai CM, Ming R, Yu Q, Jian J (2010) Integration of genetic and cytological maps and development of a pachytene chromosome-based karyotype in papaya. Trop Plant Biol 3:155–170CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2014

Authors and Affiliations

  1. 1.Department of Plant BiologyUniversity of Illinois at Urbana-ChampaignUrbanaUSA

Personalised recommendations