Abstract
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.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
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 14:259–271
Arumuganathan K, Earle ED (1991) Nuclear DNA content of some important plant species. Plant Mol Biol Rep 93:208–219
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):779–794
Bert PF, Charme G, Sourdille P, Hayward MD (1999) A high-density molecular map for ryegrass (Lolium perenne). Theor Appl Genet 99:445–452
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 52:716–725
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 48:767–790
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):425–431
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 78:495–504
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):2481–2491
Copenhaver GP, Nickel K, Kuromori T, Benito MI, Kaul S et al (1999) Genetic definition and sequence analysis of Arabidopsis centromeres. Science 286:2468–2474
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 152:1137–1172
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 106:107–111
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 125:1325–1341
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 10:1466–1472
Grodzieker T, Williams J, Sharp P, Sambrook J (1974) Physical mapping of temperature sensitive mutations of adenovirus. Cold Spring Harb Symp Quant Biol 39:439–446
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 99:254–271
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 148:479–494
Hofmeyr JDJ (1938) Genetical studies of Carica papaya L. South Afr J Sci 35:300–304
Hofmeyr JDJ (1939) Sex-linked inheritance in Carica papaya L. South Afr J Sci 36:283–285
Hofmeyr JDJ (1967) Some genetic breeding aspects of Carica papaya L. Agron Trop 17:345–351
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 37:537–543
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 10:789–807
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 427:348–352
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 103:491–507
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 166:419–436
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):1432–11436
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 105:726–735
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 102:892–899
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 452:991–996
Morgante M, Olivieri AM (1993) PCR-amplified microsatellites as markers in plant genetics. Plant J 1:175–182
Parasni AS, Gupta VS, Tamhankar SA, Ranjekar PK (2000) A highly reliable sex diagnostic PCR assay for mass screening of papaya seedlings. Mol Breed 6:337–344
Paterson A, Bowers JE, Burow MD, Draye X, Elsik CG et al (2000) Comparative genomics of plant chromosomes. Plant Cell 12:1523–1539
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):1509–1531
Peters JL, Constandt H, Neyt P, Cnops G, Zethof J et al (2001) A physical amplified fragment-length polymorphism map of Arabidopsis. Plant Physiol 127:1579–1589
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 101:948–955
Sondur SN, Manshardt RM, Stiles JI (1995) Genetics of growth rate and flowering time in papaya (Carica papaya L.). J Quant Trait Loci. http://probe.nalusda.gov:8000/otherdocs/jqtl/1995-04/jqtl8r2.html
Sondur SN, Manshardt RM, Stiles JI (1996) A genetic linkage map of papaya based on randomly amplified polymorphic DNA markers. Theor Appl Genet 93:547–553
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 85:697–701
Storey WB (1953) Genetics of papaya. J Hered 44:70–78
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 132:1141–1160
Tanksley SD, Ganal MW, Martin GB (1995) Chromosome landing: a paradigm for map-based gene cloning in plants with large genomes. Trends Genet 11:63–68
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 104:281–285
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):1013–1021
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 23:4407–4414
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 99:921–935
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 3:171–181
Wikstrom N, Savolainen V, Chase MW (2001) Evolution of the angiosperms: calibrating the family tree. Proc Biol Sci 268:2211–2220
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 18:6531–6653
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 278:177–185
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):124–132
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 10:371
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 18:1938–1943
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 3:155–170
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2014 Springer Science+Business Media New York
About this chapter
Cite this chapter
Han, J., Ming, R. (2014). Molecular Genetic Mapping of Papaya. 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_8
Download citation
DOI: https://doi.org/10.1007/978-1-4614-8087-7_8
Published:
Publisher Name: Springer, New York, NY
Print ISBN: 978-1-4614-8086-0
Online ISBN: 978-1-4614-8087-7
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)