, Volume 164, Issue 1, pp 37–51

Linkage mapping and genome analysis in a Saccharum interspecific cross using AFLP, SRAP and TRAP markers

  • Sreedhar Alwala
  • Collins A. Kimbeng
  • John C. Veremis
  • Kenneth A. Gravois


Framework genetic linkage maps of two progenitor species of cultivated sugarcane, Saccharum officinarum ‘La Striped’ (2n = 80) and S. spontaneum ‘SES 147B’ (2n = 64) were constructed using amplified fragment length polymorphism (AFLP), sequence related amplified polymorphism (SRAP), and target region amplification polymorphism (TRAP) markers. The mapping population was comprised of 100 F1 progeny derived from the interspecific cross. A total of 344 polymorphic markers were generated from the female (S. officinarum) parent, out of which 247 (72%) were single-dose (segregating in a 1:1 ratio) and 33 (9%) were double-dose (segregating in a 3.3:1 ratio) markers. Sixty-four (19%) markers deviated from Mendelian segregation ratios. In the S. spontaneum genome, out of a total of 306 markers, 221 (72%) were single-dose, 43 (14%) were double-dose, and 42 markers (14%) deviated from Mendelian segregation ratios. Linkage maps with Kosambi map distances were constructed using a LOD score ≥5.0 and a recombination threshold of 0.45. In Saccharum officinarum, 146 markers were linked to form 49 linkage groups (LG) spanning 1732 cM whereas, in S. spontaneum, 121 markers were linked to form 45 LG spanning 1491 cM. The estimated genome size of S. officinarum ‘La Striped’ was 2448 cM whereas that of S. spontaneum ‘SES 147B’ was 3232 cM. Based on the two maps, genome coverage was 69% in S. officinarum and 46% in S. spontaneum. The S. officinarum parent ‘La Striped’ behaved like an auto-allopolyploid whereas S. spontaneum ‘SES 147B’ behaved like a true autopolyploid. Although a large disparity exists between the two genomes, the existence of simple duplex markers, which are heterozygous in both parents and segregate 3:1 in the progeny, indicates that pairing and recombination can occur between the two genomes. The study also revealed that, compared with AFLP, the SRAP and TRAP markers appear less effective at generating a large number of genome-wide markers for linkage mapping in sugarcane. However, SRAP and TRAP markers can be useful for QTL mapping because of their ability to target gene-rich regions of the genome, which is a focus of our future research.


Saccharum AFLP SRAP TRAP markers Linkage map Segregation distortion 


  1. Aitken KS, Jackson PA, McIntyre CL (2005) A combination of AFLP and SSR markers provide extensive map coverage and identification of homo(eo)logous linkage groups in a sugarcane cultivar. Theor Appl Genet 110:789–801PubMedCrossRefGoogle Scholar
  2. Aitken KS, Jackson PA, McIntyre CL (2007) Construction of genetic linkage map of Saccharum officinarum incorporating both simplex and duplex markers to increase genome coverage. Genome 50:742–756PubMedCrossRefGoogle Scholar
  3. Al-Janabi SM, Honeycutt RJ, McClelland M, Sobral BWS (1993) A genetic linkage map of Saccharum spontaneum L. ‘SES 208’. Genetics 134:1249–1260PubMedGoogle Scholar
  4. Alwala S, Suman A, Arro JA, Veremis JC, Kimbeng CA (2006a) Target Region Amplification Polymorphism (TRAP) for assessing genetic diversity in sugarcane germplasm collections. Crop Sci 46:448–455CrossRefGoogle Scholar
  5. Alwala S, Kimbeng CA, Gravois KA, Bischoff KP (2006b) TRAP, a new tool for sugarcane breeding: comparison with AFLP and coefficient of parentage. Sugar Cane Intern 24:11–21Google Scholar
  6. Barreneche T, Bodenes C, Lexer C, Trontin JF, Fluch S, Streiff R, Plomion C, Roussel G, Steinkellner H, Burg K, Favre JM, Glossl J, Kremer A (1998) A genetic linkage map of Quercus robur L. (pedunculate oak) based on RAPD, SCAR, microsatellite, minisatellite, isozyme and 55 rDNA markers. Theor Appl Genet 97:1090–1103CrossRefGoogle Scholar
  7. Berding N, Roach BT (1987) Germplasm, collection, maintenance and use. In: Heinz DJ (ed) Sugarcane improvement through breeding. Elsevier, Amsterdam, pp 143–210Google Scholar
  8. Bhat SR, Gill BS (1985) The implication of 2n egg gametes in nobilisation and breeding of sugarcane. Euphytica 34:377–384CrossRefGoogle Scholar
  9. Bishop DT, Cannings C, Skolnick M, Williamson JA (1983) The number of polymorphic clones required to map the human genome. In: Weir BS (ed) Statistical analysis of DNA sequence data. Marcel Dekker, New York, pp 118–200Google Scholar
  10. Bremer G (1961) Problems in breeding and cytology of sugarcane. Euphytica 10:59–78CrossRefGoogle Scholar
  11. Cedar H (1988) DNA methylation and gene activity. Cell 53:3–4PubMedCrossRefGoogle Scholar
  12. D’Hont A, Grivet L, Feldmann P, Rao PS, Berding N, Glazmann JC (1996) Characterisation of the double genome structure of modern sugarcane cultivars (Saccharum spp.) by molecular cytogenetics. Mol Gen Genet 250:405–413PubMedGoogle Scholar
  13. D’Hont A, Ison D, Alix K, Roux C, Glazmann JC (1998) Determination of basic chromosome numbers in the genus Saccharum by physical mapping of ribosomal RNA genes. Genome 41:221–225CrossRefGoogle Scholar
  14. da Silva JAG, Sorrells ME, Burnquist W, Tanksley SD (1993) RFLP linkage map and genome analysis of Saccharum spontaneum. Genome 36:782–791PubMedCrossRefGoogle Scholar
  15. Daniels J, Roach BT (1987) Taxonomy and evolution in sugarcane. In: Heinz DJ (ed) Sugarcane improvement through breeding. Elsevier, Amsterdam, pp 7–84Google Scholar
  16. Daniels J, Smith P, Paton N, Williams CA (1975) The origin of the genus Saccharum. Sugarcane Breed News 36:24–39Google Scholar
  17. Deren CW (1995) Genetic base of U.S. mainland sugarcane. Crop Sci 35:1195–1199CrossRefGoogle Scholar
  18. deVicente MC, Tanksley SD (1993) QTL analysis of transgressive segregation in an interspecific tomato cross. Genetics 134:585–596PubMedGoogle Scholar
  19. Dietrich WF, Miller J, Steen R, Merchant MA, Damron Boles D et al (1996) A comprehensive genetic map of the mouse genome. Nature (London) 380:149–152CrossRefGoogle Scholar
  20. Edmé SJ, Comstock JC, Miller JD, Tai PYP (2005) Determination of DNA content and genome size in field grown sugarcane interspecific hybrids and genotypes. J Am Soc Sugar Cane Technol 5:1–7Google Scholar
  21. Edmé SJ, Glynn NG, Comstock JC (2006) Genetic segregation of microsatellite markers in Saccharum officinarum and S. spontaneum. Heredity 97:366–375PubMedCrossRefGoogle Scholar
  22. Ferriol M, Picó B, Nuez F (2003) Genetic diversity of a germplasm collection of Cucurbita pepo using SRAP and AFLP markers. Theor Appl Genet 107:271–282PubMedCrossRefGoogle Scholar
  23. Frewen BE, Chen THH, Howe GT, Davis J, Rhode A, Boerjan W, Bradshaw HD (2000) Quantitative trait loci and candidate gene mapping of bud set and bud flush in Populus. Genetics 154:837–845PubMedGoogle Scholar
  24. Garcia AAF, Kido EA, Meza AN, Souza HMB, Pinto LR, Pastina MM, Leite CS, da Silva JAG, Ulian EC, Figueira A, Souza AP (2006) Development of an integrated genetic map of a sugarcane (Saccharum spp.) commercial cross, based on a maximum-likelihood approach for estimation of linkage and linkage phases. Theor Appl Genet 112:298–314PubMedCrossRefGoogle Scholar
  25. Grattapaglia D, Sederoff R (1994) Genetic linkage maps of Eucalyptus grandis and Eucalyptus urophylla using a pseudo-testcross: mapping strategy and RAPD markers. Genetics 137:1121–1137PubMedGoogle Scholar
  26. Guimarães CT, Honeycutt RJ, Sills GR, Sobral BWS (1999) Genetic maps of Saccharum officinarum L. and Saccharum robustum Brandes & Jew. Ex Grassl. Genet Mol Biol 22:125–132CrossRefGoogle Scholar
  27. Hoarau JY, Offmann B, D’Hont A, Risterucci AM, Roques D, Glaszmann JC, Grivet L (2001) Genetic dissection of a modern sugarcane cultivar (Saccharum spp.). I. Genome mapping with AFLP markers. Theor Appl Genet 103:84–97CrossRefGoogle Scholar
  28. Hu JG, Vick BA (2003) Target region amplification polymorphism: a novel marker technique for plant genotyping. Plant Mol Biol Rep 21:289–294CrossRefGoogle Scholar
  29. Hulbert SH, Ilot TW, Egg EJL, Lincolne SE, Lander S, Michelmore RW (1988) Genetic analysis of the fungus Bremia lactucae using restriction fragment length polymorphisms. Genetics 120:947–958PubMedGoogle Scholar
  30. Jackson PA (2005) Breeding for improved sugar content in sugarcane. Field Crops Res 92:277–290CrossRefGoogle Scholar
  31. Jannoo N, Grivet L, Seguin M, Paulet F, Domaingue R, Rao PS, Dookun A, D’Hont A, Glazmann JC (1999) Molecular investigation of the genetic base of sugarcane cultivars. Theor Appl Genet 99:171–184CrossRefGoogle Scholar
  32. Kubisiak TL, Nelson CD, Nance WL, Stine M (1995) RAPD linkage mapping in a longleaf pine x slash pine F1 family. Theor Appl Genet 90:1119–1127CrossRefGoogle Scholar
  33. Kuramoto N, Tomaru N, Murai M, Ohba K (1997) Linkage analysis of isozyme and dwarf loci, and detection of lethal genes in sugi (Cryptomeria japonica D. Don). Breed Sci 47:259–266Google Scholar
  34. Li G, Quiros CF (2001) Sequence related amplified polymorphism (SRAP), a new marker system based on a simple PCR reaction: its application to mapping and gene tagging in Brassica. Theor Appl Genet 103:455–461CrossRefGoogle Scholar
  35. Liu ZH, Anderson JA, Hu J, Friesen TL, Rasmussen TL, Faris JD (2005) A wheat intervarietal genetic linkage map based on microsatellite and target region amplified polymorphism markers and its utility for detecting quantitative trait loci. Theor Appl Genet 111:782–794PubMedCrossRefGoogle Scholar
  36. Maliepaard C, Alston FH, van Arkel G, Brown LM, Chevreau E, Dunemann F, Evans KM, Gardiner S, Guilford P, van Heusden AW, Janse J, Laurens F, Lynn JR, Manganaris AG, den Nijs APM, Periam N, Rikkereink E, Roche P, Ryder C, Sanvasini S, Schmidt H, Tartarini S, Verhaegh JJ, Vrielink-van Ginkel M, King GJ (1998) Aligning male and female linkage maps of apple (Malus pumila Mill.) using multi-allelic markers. Theor Appl Genet 97:60–73CrossRefGoogle Scholar
  37. Mather K (1957) The measurement of linkage in heredity. Methuen, LondonGoogle Scholar
  38. Mignouna HD, Mank RA, Ellis THN, van den Bosch N, Asiedu R, Ng SYC, Pelemann J (2002a) A genetic linkage map of Guinea yam (Dioscorea rotundata Poir.) based on AFLP markers. Theor Appl Genet 105:716–725PubMedCrossRefGoogle Scholar
  39. Mignouna HD, Mank RA, Ellis THN, van den Bosch N, Asiedu R, Abang M, Pelemann J et al (2002b) 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
  40. Miklas PN, Hu J, Grünwald NJ, Larsen KM (2006) Potential application of TRAP (Targeted Region Amplified Polymorphism) markers for mapping and tagging disease resistance traits in common bean. Crop Sci 46:910–916CrossRefGoogle Scholar
  41. Ming R, Liu SC, Lin YR, da Silva JAG, Wilson W, Braga D, van Devnze A, Wenslaff F, Wu KK, Moore PH, Burnquist W, Sorrells ME, Irvine JE, Paterson AH (1998) Detailed alignment of Saccharum and Sorghum chromosomes: comparative organization of closely related diploid and polyploid genomes. Genetics 150:1663–1682PubMedGoogle Scholar
  42. Mudge J, Andersen WR, Kehrer RL, Fairbanks DJ (1996) A RAPD genetic map of Saccharum officinarum. Crop Sci 36:1362–1366CrossRefGoogle Scholar
  43. Nikaido AM, Ujino T, Iwata H, Yoshimura K, Yoshimura H, Suyama Y, Murai M, Nagasaka K, Tsumura Y (2000) AFLP and CAPS linkage maps of Cryptomeria japonica. Theor Appl Genet 100:825–831CrossRefGoogle Scholar
  44. Panje RR, Babu CN (1960) Studies in Saccharum spontaneum distribution and geographical association of chromosome numbers. Cytologia 25:152–172Google Scholar
  45. Piperidis G, D’Hont A (2001) Chromosome composition analysis of various Saccharum interspecific hybrids by genomic in situ hybridisation (GISH). Int Soc Sugar Cane Technol Cong 11:565Google Scholar
  46. Reffay N, Jackson PA, Aitken KS, Hoarau JY, D’Hont A, Besse P, McIntyre CL (2005) Characterisation of genome regions incorporated from an important wild relative into Australian sugarcane. Mol Breed 15:367–381CrossRefGoogle Scholar
  47. Roach BT (1972) Nobilization of sugarcane. Proc Int Soc Sugar Cane Technol 14:206–216Google Scholar
  48. Sreenivasan TV, Ahloowalia BS, Heinz DJ (1987) Cytogenetics. In: Heinz DJ (ed) Sugarcane improvement through breeding. Elsevier, Amsterdam, pp 211–253Google Scholar
  49. Suman A, Kimbeng CA (2007) Molecular diversity among ancestral species of Saccharum and the proportion of diversity represented in major Louisiana commercial breeding clones. ASA Southern Branch 2007 Annual Meeting February 4–6, 2007 Mobile, ALGoogle Scholar
  50. Tanksley SD, Nelson JC (1996) Advanced backcross QTL analysis: a method for the simultaneous discovery and transfer of valuable QTLs from unadapted germplasm into elite breeding lines. Theor Appl Genet 92:191–203CrossRefGoogle Scholar
  51. van Heusden AW, van Ooijen JW, Vrielink-van Ginkel R, Verbeek WHJ, Wietsma WA, Kik C (2000) A genetic map of an interspecific cross in Allium based on amplified fragment length polymorphism (AFLP™) markers. Theor Appl Genet 100:118–126CrossRefGoogle Scholar
  52. van Ooijen JW, Voorrips RE (2001) Joinmap 3.0. Software for the calculation of genetic linkage maps. Plant Research International, Wageningen, The NetherlandsGoogle Scholar
  53. Vos P, Hogers R, Bleeker M, Reijan M, van de Lee T, Hornes M, Freijters A, Pot J, Peleman J, Kuiper M, Zabeau M (1995) AFLP: a new technique for DNA fingerprinting. Nucl Acid Res 23:4407–4414CrossRefGoogle Scholar
  54. Wu KK, Burnquist W, Sorrells ME, Tew TL, Moore PH, Tanksley SD (1992) The detection and estimation of linkage in polyploids using single-dose restriction fragments. Theor Appl Genet 83:294–300CrossRefGoogle Scholar
  55. Young WP, Schupp JM, Keim P (1999) DNA methylation and AFLP marker distribution in the soybean genome. Theor Appl Genet 99:785–792CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2007

Authors and Affiliations

  • Sreedhar Alwala
    • 1
  • Collins A. Kimbeng
    • 1
  • John C. Veremis
    • 2
    • 3
  • Kenneth A. Gravois
    • 4
  1. 1.School of Plant, Environmental and Soil SciencesLouisiana State University Agricultural CenterBaton RougeUSA
  2. 2.USDA-ARS, SRRC, Sugarcane Research UnitHoumaUSA
  4. 4.Sugar Research Station, Louisiana Agricultural Experiment StationLouisiana State University Agricultural CenterSt. GabrielUSA

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