Skip to main content
Log in

SSR and EST-SSR-based genetic linkage map of cassava (Manihot esculenta Crantz)

  • Original Paper
  • Published:
Theoretical and Applied Genetics Aims and scope Submit manuscript

Abstract

Simple sequence repeat (SSR) markers provide a powerful tool for genetic linkage map construction that can be applied for identification of quantitative trait loci (QTL). In this study, a total of 640 new SSR markers were developed from an enriched genomic DNA library of the cassava variety ‘Huay Bong 60’ and 1,500 novel expressed sequence tag-simple sequence repeat (EST-SSR) loci were developed from the Genbank database. To construct a genetic linkage map of cassava, a 100 F1 line mapping population was developed from the cross Huay Bong 60 by ‘Hanatee’. Polymorphism screening between the parental lines revealed that 199 SSRs and 168 EST-SSRs were identified as novel polymorphic markers. Combining with previously developed SSRs, we report a linkage map consisted of 510 markers encompassing 1,420.3 cM, distributed on 23 linkage groups with a mean distance between markers of 4.54 cM. Comparison analysis of the SSR order on the cassava linkage map and the cassava genome sequences allowed us to locate 284 scaffolds on the genetic map. Although the number of linkage groups reported here revealed that this F1 genetic linkage map is not yet a saturated map, it encompassed around 88% of the cassava genome indicating that the map was almost complete. Therefore, sufficient markers now exist to encompass most of the genomes and efficiently map traits in cassava.

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

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1

Similar content being viewed by others

References

  • Awoleye F, Duren M, Dolezel J, Novak FJ (1994) Nuclear DNA content and in vitro induced somatic polyploidization cassava (Manihot esculenta Crantz) breeding. Euphytica 76:195–202

    Article  CAS  Google Scholar 

  • Benbouza H, Jacquemin J, Baudoin J, Mergeai G (2006) Optimization of a reliable, fast, cheap and sensitive silver staining method to detect SSR markers in polyacrylamide gels. Biotechnol Agron Soc Environ 10:77–81

    CAS  Google Scholar 

  • Bennett MD, Smith JB, Heslop-Harrison JS (1982) Nuclear DNA amounts in angiosperms. Proc R Soc Lond Ser B Biol Sci 179–199

  • Butcher PA, Decroocq S, Gray Y, Moran GF (2000) Development, inheritance and cross-species amplification of microsatellite markers from Acacia mangium. Theor Appl Genet 101:1282–1290

    Article  CAS  Google Scholar 

  • Chavarriaga-Aguirre PP, Maya MM, Bonierbale MW, Kresovich S, Fregene MA, Tohme J, Kochert G (1998) Microsatellites in cassava (Manihot esculenta Crantz): discovery, inheritance and variability. Theor Appl Genet 97:493–501

    Article  CAS  Google Scholar 

  • Chen X, Xia Z, Fu Y, Lu C, Wang W (2010) Constructing a genetic linkage map using an F1 population of non-inbred parents in cassava (Manihot esculenta Crantz). Plant Mol Biol Report. doi:10.1007/s11105-010-0198-9

  • Cho YG, Ishii T, Temnykh S, Chen X, Lipovich L, McCouch SR, Park WD, Ayres N, Cartinhour S (2000) Diversity of microsatellites derived from genomic libraries and GenBank sequences in rice (Oryza sativa L.). Theor Appl Genet 100:713–722

    Article  CAS  Google Scholar 

  • Collard BC, Mackill DJ (2008) Marker-assisted selection: an approach for precision plant breeding in the twenty-first century. Philos Trans R Soc Lond B Biol Sci 363:557–572

    Article  PubMed  CAS  Google Scholar 

  • Collard B, Jahufer M, Brouwer J, Pang E (2005) An introduction to markers, quantitative trait loci (QTL) mapping and marker-assisted selection for crop improvement: the basic concepts. Euphytica 142:169–196

    Article  CAS  Google Scholar 

  • El-Sharkawy MA (2004) Cassava biology and physiology. Plant Mol Biol 56:481–501

    Article  PubMed  CAS  Google Scholar 

  • Feng SP, Li WG, Huang HS, Wang JY, Wu YT (2009) Development, characterization and cross-species/genera transferability of EST-SSR markers for rubber tree (Hevea brasiliensis). Mol Breed 23:85–97

    Article  CAS  Google Scholar 

  • Field D, Wills C (1996) Long, polymorphic microsatellites in simple organisms. Proc R Soc Lond 263:209–215

    Article  CAS  Google Scholar 

  • Fregene M, Angel F, Gomez R, Rodriguez F, Chavarriaga P, Roca W, Tohme J, Bonierbale M (1997) A molecular genetic map of cassava (Manihot esculenta Crantz). Theor Appl Genet 95:431–441

    Article  CAS  Google Scholar 

  • Gupta P, Varshney R (2000) The development and use of microsatellite markers for genetic analysis and plant breeding with emphasis on bread wheat. Euphytica 113:163–185

    Article  CAS  Google Scholar 

  • Hackett CA, Wachira FN, Paul S, Powell W, Waugh R (2000) Construction of a genetic linkage map for Camellia sinensis (tea). Heredity 85:346–355

    Article  PubMed  CAS  Google Scholar 

  • He G, Meng R, Newman M, Gao G, Pittman R, Prakash CS (2003) Microsatellites as DNA markers in cultivated peanut (Arachis hypogaea L.). BMC Plant Biol 3:3

    Article  PubMed  Google Scholar 

  • Hulbert SH, Ilott TW, Legg EJ, Lincoln SE, Lander ES, Michelmore RW (1988) Genetic analysis of the fungus, Bremia lactucae, using restriction fragments length polymorphisms. Genetics 120:947–958

    PubMed  CAS  Google Scholar 

  • Kashi Y, King D, Soller M (1997) Simple sequence repeats as a source of quantitative genetic variation. Trends Genet 13:74–78

    Article  PubMed  CAS  Google Scholar 

  • Kosambi DD (1944) The estimation of map distance from recombination values. Ann Eugen Lond 12:172–175

    Google Scholar 

  • Kunkeaw S, Tangphatsornruang S, Smith DR, Triwitayakorn K (2010a) Genetic linkage map of cassava (Manihot esculenta Crantz) based on AFLP and SSR markers. Plant Breed 129:112–115

    Article  CAS  Google Scholar 

  • Kunkeaw S, Yoocha T, Sraphet S, Boonchanawiwat A, Boonseng O, Lightfoot DA, Triwitayakorn K, Tangphatsornruang S (2010b) Construction of a genetic linkage map using simple sequence repeat markers from expressed sequence tags for cassava (Manihot esculenta Crantz). Mol Breed 10. doi:10.1007/s11032-010-9414-4

  • La Rota M, Kantety R, Yu J-K, Sorrells M (2005) Nonrandom distribution and frequencies of genomic and EST-derived microsatellite markers in rice, wheat, and barley. BMC Genomics 6:23

    Article  PubMed  Google Scholar 

  • Li YC, Korol AB, Fahima T, Beiles A, Nevo E (2002) Microsatellites: genomic distribution, putative functions and mutational mechanisms: a review. Mol Ecol 11:2453–2465

    Article  PubMed  CAS  Google Scholar 

  • Mba REC, Stephenson P, Edwards K, Melzer S, Nkumbira J, Gullberg U, Apel K, Gale M, Tohme J, Fregene MF (2001) Simple sequence repeat (SSR) markers survey of the cassava (Manihot esculenta Crantz) genome: towards an SSR-based molecular genetic map of cassava. Theor Appl Genet 102:21–31

    Article  CAS  Google Scholar 

  • McCouch SR, Teytelman L, Xu Y, Lobos KB, Clare K, Walton M, Fu B, Maghirang R, Li Z, Xing Y, Zhang Q, Kono I, Yano M, Fjellstrom R, DeClerck G, Schneider D, Cartinhour S, Ware D, Stein L (2002) Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.). DNA Res 9:199–207

    Article  PubMed  CAS  Google Scholar 

  • Morgante M, Hanafey M, Powell W (2002) Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes. Nat Genet 30:194–200

    Article  PubMed  CAS  Google Scholar 

  • Nunome T, Negoro S, Miyatake K, Yamaguchi H, Fukuoka H (2006) A protocol for the construction of microsatellite enriched genomic library. Plant Mol Biol Rep 24:305–312

    Article  CAS  Google Scholar 

  • Okogbenin E, Marin J, Fregene M (2006) An SSR-based molecular genetic map of cassava. Euphytica 147:433–440

    Article  CAS  Google Scholar 

  • Raji AA, Anderson JV, Kolade OA, Ugwu CD, Dixon AG, Ingelbrecht IL (2009) Gene-based microsatellites for cassava (Manihot esculenta Crantz): prevalence, polymorphisms, and cross-taxa utility. BMC Plant Biol 9:118

    Article  PubMed  Google Scholar 

  • Ribaut J-M, Hoisington D (1998) Marker-assisted selection: new tools and strategies. Trends Plant Sci 3:236–239

    Article  Google Scholar 

  • Ritschel PS, Lins TC, Tristan RL, Buso GS, Buso JA, Ferreira ME (2004) Development of microsatellite markers from an enriched genomic library for genetic analysis of melon (Cucumis melo L.). BMC Plant Biol 4:9

    Google Scholar 

  • Rudd S (2003) Expressed sequence tags: alternative or complement to whole genome sequences? Trends Plant Sci 8:321–329

    Article  PubMed  CAS  Google Scholar 

  • Saha MC, Cooper JD, Mian MA, Chekhovskiy K, May GD (2006) Tall fescue genomic SSR markers: development and transferability across multiple grass species. Theor Appl Genet 113:1449–1458

    Article  PubMed  CAS  Google Scholar 

  • Sato S, Isobe S, Asamizu E, Ohmido N, Kataoka R, Nakamura Y, Kaneko T, Sakurai N, Okumura K, Klimenko I, Sasamoto S, Wada T, Watanabe A, Kohara M, Fujishiro T, Tabata S (2005) Comprehensive structural analysis of the genome of red clover (Trifolium pratense L.). DNA Res 12:301–364

    Article  PubMed  CAS  Google Scholar 

  • Sharopova N, McMullen MD, Schultz L, Schroeder S, Sanchez-Villeda H, Gardiner J, Bergstrom D, Houchins K, Melia-Hancock S, Musket T, Duru N, Polacco M, Edwards K, Ruff T, Register JC, Brouwer C, Thompson R, Velasco R, Chin E, Lee M, Woodman-Clikeman W, Long MJ, Liscum E, Cone K, Davis G, Coe EH (2002) Development and mapping of SSR markers for maize. Plant Mol Biol 48:463–481

    Article  PubMed  CAS  Google Scholar 

  • Shultz JL, Kazi S, Bashir R, Afzal JA, Lightfoot DA (2007) The development of BAC-end sequence-based microsatellite markers and placement in the physical and genetic maps of soybean. Theor Appl Genet 114:1081–1090

    Article  PubMed  CAS  Google Scholar 

  • Song QJ, Marek LF, Shoemaker RC, Lark KG, Concibido VC, Delannay X, Specht JE, Cregan PB (2004) A new integrated genetic linkage map of the soybean. Theor Appl Genet 109:122–128

    Article  PubMed  CAS  Google Scholar 

  • Song Q, Shi J, Singh S, Fickus E, Costa J, Lewis J, Gill B, Ward R, Cregan P (2005) Development and mapping of microsatellite (SSR) markers in wheat. Theor Appl Genet 110:550–560

    Article  PubMed  CAS  Google Scholar 

  • Tangphatsornruang S, Sraphet S, Singh R, Okogbenin E, Fregene M, Triwitayakorn K (2008) Development of polymorphic markers from expressed sequence tags of Manihot esculenta Crantz. Mol Ecol Resour 8:682–685

    Article  CAS  Google Scholar 

  • Temnykh S, DeClerck G, Lukashova A, Lipovich L, Cartinhour S, McCouch S (2001) Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations, and genetic marker potential. Genome Res 11:1441–1452

    Article  PubMed  CAS  Google Scholar 

  • Tsukazaki H, Nunome T, Fukuoka H, Kanamori H, Kono I, Yamashita K-i, Wako T, Kojima A (2007) Isolation of 1,796 SSR clones from SSR-enriched DNA libraries of bunching onion (Allium fistulosum). Euphytica 157:83–94

    Article  CAS  Google Scholar 

  • Van Ooijen JW, Voorrips RE (2001) JoinMap 3.0, Software for the calculation of genetic linkage maps. Plant Research International, Wageningen

    Google Scholar 

  • Varshney RK, Graner A, Sorrells ME (2005) Genic microsatellite markers in plants: features and applications. Trends Biotechnol 23:48–55

    Article  PubMed  CAS  Google Scholar 

  • Yu JK, Dake TM, Singh S, Benscher D, Li W, Gill B, Sorrells ME (2004a) Development and mapping of EST-derived simple sequence repeat markers for hexaploid wheat. Genome 47:805–818

    Article  PubMed  CAS  Google Scholar 

  • Yu JK, La Rota M, Kantety RV, Sorrells ME (2004b) EST derived SSR markers for comparative mapping in wheat and rice. Mol Genet Genomics 271:742–751

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgments

This research was supported by National Center for Genetic Engineering and Biotechnology (Thailand), Commission on Higher Education, Ministry of Education (Thailand), the Thailand Research Fund and Mahidol University. Supajit Sraphet and Athipong Boonchanawiwat were supported from Thailand Graduate Institute of Science and Technology (TGIST) for PhD and MS studies, respectively. The cassava genome sequence was downloaded from “Cassava Genome Project 2009 http://www.phytozome.net/cassava”.

Author information

Authors and Affiliations

Authors

Corresponding authors

Correspondence to Sithichoke Tangphatsornruang or Kanokporn Triwitayakorn.

Additional information

Communicated by A. Bervillé.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Sraphet, S., Boonchanawiwat, A., Thanyasiriwat, T. et al. SSR and EST-SSR-based genetic linkage map of cassava (Manihot esculenta Crantz). Theor Appl Genet 122, 1161–1170 (2011). https://doi.org/10.1007/s00122-010-1520-5

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00122-010-1520-5

Keywords

Navigation