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Construction of a genetic linkage map using simple sequence repeat markers from expressed sequence tags for cassava (Manihot esculenta Crantz)

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Abstract

Cassava (Manihot esculenta) is an economically important crop that is grown in tropical and sub-tropical regions. Use of molecular technology for genetic improvement of cassava has been limited by the lack of a large set of DNA markers and a genetic map. Therefore, the aims here were to develop additional simple sequence repeat (SSR) markers from the public expressed sequence tags (ESTs), and to construct a genetic linkage map. In this study, we designed 425 EST-SSR markers from sequences obtained from the cassava EST database in GenBank, and integrated them with 667 SSR markers from a microsatellite-enriched genomic sequence received from the International Center for Tropical Agriculture (CIAT). Of these, 107 EST-SSR and 500 genomic SSR primer pairs showed polymorphic patterns when screened in two cassava varieties, Hauy Bong 60 and Hanatee, which were used as female and male parental lines, respectively. Within the 107 and 500 primer pairs, 81 and 226 EST-SSR and SSR primer pairs were successfully genotyped with 100 samples of F1 progeny, respectively. The results showed 20 linkage groups consisting of 211 markers—56 EST-SSR and 155 SSR markers—spanning 1,178 cM, with an average distance between markers of 5.6 cM and about 11 markers per linkage group. These novel EST-SSR markers provided genic PCR-based co-dominant markers that were useful, reliable and economical. The EST-SSRs were used together with SSR markers to construct the cassava genetic linkage map which will be useful for the identification of quantitative trait loci controlling the traits of interest in cassava breeding programs.

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References

  • Adams M, Kelley J, Gocayne J, Dubnick M, Polymeropoulos M, Xiao H, Merril C, Wu A, Olde B, Moreno R (1991) Complementary DNA sequencing: expressed sequence tags and human genome project. Science 252:1651–1656

    Article  CAS  PubMed  Google Scholar 

  • Aggarwal R, Hendre P, Varshney R, Bhat P, Krishnakumar V, Singh L (2007) Identification, characterization and utilization of EST-derived genic microsatellite markers for genome analyses of coffee and related species. Theor Appl Genet 114:359–372

    Article  CAS  PubMed  Google Scholar 

  • Akagi H, Yokozeki Y, Inagaki A, Fujimura T (1997) Highly polymorphic microsatellites of rice consist of AT repeats, and a classification of closely related cultivars with these microsatellite loci. Theor Appl Genet 94:61–67

    Article  CAS  PubMed  Google Scholar 

  • Akkaya MS, Bhagwat AA, Cregan PB (1992) Length polymorphisms of simple sequence repeat DNA in soybean. Genetics 132:1131–1139

    CAS  PubMed  Google Scholar 

  • Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410

    CAS  PubMed  Google Scholar 

  • Anderson JV, Delseny M, Fregene MA, Jorge V, Mba C, Lopez C, Restrepo S, Soto M, Piegu B, Verdier V, Cooke R, Tohme J, Horvath DP (2004) An EST resource for cassava and other species of Euphorbiaceae. Plant Mol Biol 56:527–539

    Article  PubMed  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 

  • Cardle L, Ramsay L, Milbourne D, Macaulay M, Marshall D, Waugh R (2000) Computational and experimental characterization of physically clustered simple sequence repeats in plants. Genetics 156:847–854

    CAS  PubMed  Google Scholar 

  • Chen C, Zhou P, Choi Y, Huang S, Gmitter F (2006) Mining and characterizing microsatellites from citrus ESTs. Theor Appl Genet 112:1248–1257

    Article  CAS  PubMed  Google Scholar 

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

    Google Scholar 

  • Dreisigacker S, Zhang P, Warburton ML, Van Ginkel M, Hoisington D, Bohn M, Melchinger AE (2004) SSR and pedigree analyses of genetic diversity among CIMMYT wheat lines targeted to different megaenvironments. Crop Sci 44:381–388

    Article  CAS  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Feng S, Li W, Huang H, Wang J, Wu Y (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 

  • Folta KM, Staton M, Stewart PJ, Jung S, Bies DH, Jesdurai C, Main D (2005) Expressed sequence tags (ESTs) and simple sequence repeat (SSR) markers from octoploid strawberry (Fragaria x ananassa). BMC Plant Biol 5:12

    Article  PubMed  Google Scholar 

  • Gao L, Tang J, Li H, Jia J (2003) Analysis of microsatellites in major crops assessed by computational and experimental approaches. Mol Breed 12:245–261

    Article  CAS  Google Scholar 

  • Jung S, Abbott A, Jesudurai C, Tomkins J, Main D (2005) Frequency, type, distribution and annotation of simple sequence repeats in Rosaceae ESTs. Funct Integr Genom 5:136–143

    Article  CAS  Google Scholar 

  • Kantety RV, La Rota M, Matthews DE, Sorrells ME (2002) Data mining for simple sequence repeats in expressed sequence tags from barley, maize, rice, sorghum and wheat. Plant Mol Biol 48:501–510

    Article  CAS  PubMed  Google Scholar 

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

    Google Scholar 

  • Lokko Y, Anderson J, Rudd S, Raji A, Horvath D, Mikel M, Kim R, Liu L, Hernandez A, Dixon A, Ingelbrecht I (2007) Characterization of an 18, 166 EST dataset for cassava (Manihot esculenta Crantz) enriched for drought-responsive genes. Plant Cell Rep 26:1605–1618

    Article  CAS  PubMed  Google Scholar 

  • Lopez C, Jorge V, Piégu B, Mba C, Cortes D, Restrepo S, Soto M, Laudié M, Berger C, Cooke R, Delseny M, Tohme J, Verdier V (2004) A unigene catalogue of 5700 expressed genes in cassava. Plant Mol Biol 56:541–554

    Article  PubMed  Google Scholar 

  • Lopez CE, Quesada-Ocampo LM, Bohorquez A, Duque MC, Vargas J, Tohme J, Verdier V (2007) Mapping EST-derived SSRs and ESTs involved in resistance to bacterial blight in Manihot esculenta. Genome 50:1078–1088

    Article  CAS  PubMed  Google Scholar 

  • Mba REC, Stephenson P, Edwards K, Melzer S, Nkumbira J, Gullberg U, Apel K, Gale M, Tohme J, Fregene M (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 

  • Nicot N, Chiquet V, Gandon B, Amilhat L, Legeai F, Leroy P, Bernard M, Sourdille P (2004) Study of simple sequence repeat (SSR) markers from wheat expressed sequence tags (ESTs). Theor Appl Genet 109:800–805

    Article  CAS  PubMed  Google Scholar 

  • Ohlrogge J, Benning C (2000) Unraveling plant metabolism by EST analysis. Curr Opin Plant Biol 3:224–228

    CAS  PubMed  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 

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

    Article  CAS  PubMed  Google Scholar 

  • Sambrook J, Russell D (2001) Molecular cloning: a laboratory manual, 3rd edn. Cold Spring Harbour Laboratory Press, New York

    Google Scholar 

  • Sasaki T (1995) Rice Genome, newsletter for rice genome analysis. Rice Genome Research Program, Tsukuba

    Google Scholar 

  • Shultz J, Kazi S, Afzal J, Bashir R, Lightfoot D (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  CAS  PubMed  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 Res 8:682–685

    Article  CAS  Google Scholar 

  • Thiel T, Michalek W, Varshney R, Graner A (2003) Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theor Appl Genet 106:411–422

    CAS  PubMed  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  CAS  PubMed  Google Scholar 

Download references

Acknowledgments

This research was supported by the National Center for Genetic Engineering and Biotechnology (BIOTEC), Thailand; the Commission on Higher Education, Ministry of Education, Thailand; the Thailand Research Fund, and Mahidol University. S.K. and S.S. were supported for PhD study and A.B. for MS study from Thailand Graduate Institute of Science and Technology (TGIST).

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Authors and Affiliations

  1. Institute of Molecular Biology and Genetics, Mahidol University, Salaya, Nakhonpathom, 73170, Thailand

    S. Kunkeaw, S. Sraphet, A. Boonchanawiwat & K. Triwitayakorn

  2. National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Paholyothin Road, Klong 1, Klong Luang, Pathumthani, 12120, Thailand

    T. Yoocha & S. Tangphatsornruang

  3. Rayong Filed Crop Research Center, Ministry of Agriculture and Cooperatives, Muang District, Rayong, 21150, Thailand

    O. Boonseng

  4. Southern Illinois University at Carbondale, Carbondle, IL, 62901, USA

    D. A. Lightfoot

  5. Faculty of Science, Center for Cassava Molecular Biotechnology, Mahidol University, Bangkok, 10400, Thailand

    K. Triwitayakorn & S. Tangphatsornruang

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  1. S. Kunkeaw
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  2. T. Yoocha
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  3. S. Sraphet
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  4. A. Boonchanawiwat
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  5. O. Boonseng
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  6. D. A. Lightfoot
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  7. K. Triwitayakorn
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  8. S. Tangphatsornruang
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Corresponding authors

Correspondence to K. Triwitayakorn or S. Tangphatsornruang.

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Kunkeaw, S., Yoocha, T., Sraphet, S. et al. Construction of a genetic linkage map using simple sequence repeat markers from expressed sequence tags for cassava (Manihot esculenta Crantz). Mol Breeding 27, 67–75 (2011). https://doi.org/10.1007/s11032-010-9414-4

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  • DOI: https://doi.org/10.1007/s11032-010-9414-4

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