Theoretical and Applied Genetics

, Volume 121, Issue 1, pp 1–8 | Cite as

Genome-wide identification of intron fragment insertion mutations and their potential use as SCAR molecular markers in the soybean

  • Yongjun Shu
  • Yong Li
  • Yanming Zhu
  • Zhenlei Zhu
  • Dekang Lv
  • Xi Bai
  • Hua Cai
  • Wei Ji
  • Dianjing Guo
Original Paper

Abstract

Introns often have a high probability of mutation as a result of DNA insertions and deletions (indels). In this study, 503 introns with exon-derived insertions were identified using a comprehensive search of the soybean genome. Of the 375 pairs of PCR primer sets designed for the loci in question, 161 primer sets amplified length polymorphism among nine soybean varieties and were identified as soybean gene-intron-driven functional sequence characterized amplified region (SCAR) markers. These SCAR markers are distributed among all 20 of the soybean chromosomes, and they developed from numerous genes involved in various physiological and biochemical processes that influence important agronomic traits of the soybean. The development of these novel gene-driven functional SCAR markers was fast and cost effective, and their use will facilitate molecular-assisted breeding of the soybean.

Notes

Acknowledgments

The soybean genome sequence data were produced by the US Department of Energy Joint Genome Institute (http://www.jgi.doe.gov/) in collaboration with the user community, and we would thank to them. The project was supported by the National “863” Program (2006AA100104, 2008AA10Z153), the National Transgenic Research Project (2008ZX08004), the Key Research Plan of Heilongjiang Province (GA06B103), and the Innovation Research Group of NEAU (CXT004).

Supplementary material

122_2010_1285_MOESM1_ESM.xls (32 kb)
Supplementary material 1 (XLS 32 kb)
122_2010_1285_MOESM2_ESM.xls (14 kb)
Supplementary material 2 (XLS 13 kb)

References

  1. Altschul S, Madden T, Schaffer A, Zhang J, Zhang Z, Miller W, Lipman D (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402CrossRefPubMedGoogle Scholar
  2. Berget SM, Moore C, Sharp PA (1977) Spliced segments at the 5′ terminus of adenovirus 2 late mRNA. Proc Natl Acad Sci USA 74:3171–3175CrossRefPubMedGoogle Scholar
  3. Berrebi P, Boissin E, Fang F, Cattaneo-Berrebi G (2005) Intron polymorphism (EPIC-PCR) reveals phylogeographic structure of Zacco platypus in China: a possible target for aquaculture development. Heredity 94:589–598CrossRefPubMedGoogle Scholar
  4. Bierne N, Lehnert SA, Bedier E, Bonhomme F, Moore SS (2000) Screening for intron-length polymorphisms in penaeid shrimps using exon-primed intron-crossing (EPIC)-PCR. Mol Ecol 9:233–235CrossRefPubMedGoogle Scholar
  5. Casa AM, Brouwer C, Nagel A, Wang L, Zhang Q, Kresovich S, Wessler SR (2000) Inaugural article: the MITE family heartbreaker (Hbr): molecular markers in maize. Proc Natl Acad Sci USA 97:10083–10089CrossRefPubMedGoogle Scholar
  6. Casa AM, Mitchell SE, Smith OS, Register JC 3rd, Wessler SR, Kresovich S (2002) Evaluation of Hbr (MITE) markers for assessment of genetic relationships among maize (Zea mays L.) inbred lines. Theor Appl Genet 104:104–110CrossRefPubMedGoogle Scholar
  7. Choi I-Y, Hyten DL, Matukumalli LK, Song Q, Chaky JM, Quigley CV, Chase K, Lark KG, Reiter RS, Yoon M-S, Hwang E-Y, Yi S-I, Young ND, Shoemaker RC, van Tassell CP, Specht JE, Cregan PB (2007) A soybean transcript map: gene distribution, haplotype and single-nucleotide polymorphism analysis. Genetics 176:685–696CrossRefPubMedGoogle Scholar
  8. Cregan PB, Jarvik T, Bush AL, Shoemaker RC, Lark KG, Kahler AL, Kaya N, VanToai TT, Lohnes DG, Chung J, Specht JE (1999) An integrated genetic linkage map of the soybean genome. Crop Sci 39:1464–1490Google Scholar
  9. Ferreira A, Foutz K, Keim P (2000) Soybean genetic map of RAPD markers assigned to an existing scaffold RFLP map. J Hered 91:392–396CrossRefPubMedGoogle Scholar
  10. Gupta PK, Rustgi S, Kulwal PL (2005) Linkage disequilibrium and association studies in higher plants: present status and future prospects. Plant Mol Biol 57:461–485CrossRefPubMedGoogle Scholar
  11. Hisano H, Sato S, Isobe S, Sasamoto S, Wada T, Matsuno A, Fujishiro T, Yamada M, Nakayama S, Nakamura Y, Watanabe S, Harada K, Tabata S (2007) Characterization of the soybean genome using EST-derived microsatellite markers. DNA Res 14:271–281CrossRefPubMedGoogle Scholar
  12. Hyten DL, Song Q, Zhu Y, Choi I-Y, Nelson RL, Costa JM, Specht JE, Shoemaker RC, Cregan PB (2006) Impacts of genetic bottlenecks on soybean genome diversity. Proc Natl Acad Sci USA 103:16666–16671CrossRefPubMedGoogle Scholar
  13. Keim P, Diers BW, Olson TC, Shoemaker RC (1990) RFLP mapping in soybean: association between marker loci and variation in quantitative traits. Genetics 126:735–742PubMedGoogle Scholar
  14. Keim P, Schupp JM, Travis SE, Clayton K, Zhu T, Shi L, Ferreira A, Webb DM (1997) A high-density soybean genetic map based on AFLP markers. Crop Sci 37:537–543Google Scholar
  15. Lightfoot DA, Gibson PT, Merkem K (2001) Soybean sudden death syndrome resistant soybeans, soybean cyst nematode resistant soybeans and methods of breeding and identifying resistant plants. US Patent 6300541Google Scholar
  16. Matthews BF, Devine TE, Weisemann JM, Beard HS, Lewers KS, MacDonald MH, Park Y-B, Maiti R, Lin J-J, Kuo J, Pedroni MJ, Cregan PB, Saunders JA (2001) Incorporation of sequenced cDNA and genomic markers into the soybean genetic map. Crop Sci 41:516–521CrossRefGoogle Scholar
  17. Meksem K, Ruben E, Hyten D, Triwitayakorn H, Lightfoot DA (2001) Conversion of AFLP bands into high-throughput DNA markers. Mol Genet Genomics 265:207–214CrossRefPubMedGoogle Scholar
  18. Mewes HW, Frishman D, Mayer KF, Munsterkotter M, Noubibou O, Pagel P, Rattei T, Oesterheld M, Ruepp A, Stumpflen V (2006) MIPS: analysis and annotation of proteins from whole genomes in 2005. Nucleic Acids Res 34:D169–D172CrossRefPubMedGoogle Scholar
  19. Mochizuki K, Umeda M, Ohtsubo H, Ohtsubo E (1992) Characterization of a plant SINE, p-SINE1, in rice genomes. Jpn J Genet 67:155–166CrossRefPubMedGoogle Scholar
  20. Monden Y, Naito K, Okumoto Y, Saito H, Oki N, Tsukiyama T, Ideta O, Nakazaki T, Wessler SR, Tanisaka T (2009) High potential of a transposon mPing as a marker system in japonica × japonica cross in rice. DNA Res 16:131–140CrossRefPubMedGoogle Scholar
  21. Murray MG, Thompson WF (1980) Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res 8:4321–4325CrossRefPubMedGoogle Scholar
  22. Noguera FJ, Capel J, Alvarez JI, Lozano R (2005) Development and mapping of a codominant SCAR marker linked to the andromonoecious gene of melon. Theor Appl Genet 110:714–720CrossRefPubMedGoogle Scholar
  23. Presgraves DC (2006) Intron length evolution in Drosophila. Mol Biol Evol 23:2203–2213CrossRefPubMedGoogle Scholar
  24. Rozen S, Skaletsky H (2000) Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol 132:365–386PubMedGoogle Scholar
  25. Saini N, Shultz J, Lightfoot DA (2008) Re-annotation of the physical map of Glycine max for polyploid-like regions by BAC end sequence driven whole genome shotgun read assembly. BMC Genomics 9:323CrossRefPubMedGoogle Scholar
  26. Shimada N, Nakatsuka T, Nakano Y, Kakizaki Y, Abe Y, Hikage T, Nishihara M (2009) Identification of gentian cultivars using SCAR markers based on intron-length polymorphisms of flavonoid biosynthetic genes. Sci Hortic 119:292–296CrossRefGoogle Scholar
  27. Shu Y, Li Y, Bai X, Cai H, Ji W, Zhu Y (2009) Development of soybean gene-driven functional CAPS markers from the genes’ re-sequencing information. Acta Agron Sin 35:2015–2021CrossRefGoogle Scholar
  28. Shultz JL, Kurunam D, Shopinski K, Iqbal MJ, Kazi S, Zobrist K, Bashir R, Yaegashi S, Lavu N, Afzal AJ, Yesudas CR, Kassem MA, Wu C, Zhang HB, Town CD, Meksem K, Lightfoot DA (2006) The soybean genome database (SoyGD): a browser for display of duplicated, polyploid, regions and sequence tagged sites on the integrated physical and genetic maps of Glycine max. Nucleic Acids Res 34:D758–D765CrossRefPubMedGoogle Scholar
  29. Shultz J, Kazi S, Bashir R, Afzal J, 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 114:1081–1090CrossRefPubMedGoogle Scholar
  30. 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 109:122–128CrossRefPubMedGoogle Scholar
  31. Swarbreck D, Wilks C, Lamesch P, Berardini TZ, Garcia-Hernandez M, Foerster H, Li D, Meyer T, Muller R, Ploetz L, Radenbaugh A, Singh S, Swing V, Tissier C, Zhang P, Huala E (2008) The Arabidopsis Information Resource (TAIR): gene structure and function annotation. Nucleic Acids Res 36:D1009–D1014CrossRefPubMedGoogle Scholar
  32. Tay WT, Behere GT, Heckel DG, Lee SF, Batterham P (2008) Exon-primed intron-crossing (EPIC) PCR markers of Helicoverpa armigera (Lepidoptera: Noctuidae). Bull Entomol Res 98:509–518CrossRefPubMedGoogle Scholar
  33. Voorrips RE (2002) MapChart: software for the graphical presentation of linkage maps and QTLs. J Hered 93:77–78CrossRefPubMedGoogle Scholar
  34. Wang X (2002) Phospholipase D in hormonal and stress signaling. Curr Opio Plant Biol 5:408–414CrossRefGoogle Scholar
  35. Wang X, Zhao X, Zhu J, Wu W (2005) Genome-wide investigation of intron length polymorphisms and their potential as molecular markers in rice (Oryza sativa L.). DNA Res 12:417–427CrossRefPubMedGoogle Scholar
  36. Wilson LM, Whitt SR, Ibanez AM, Rocheford TR, Goodman MM, Buckler EST (2004) Dissection of maize kernel composition and starch production by candidate gene association. Plant Cell 16:2719–2733CrossRefPubMedGoogle Scholar
  37. Xu JH, Kurata N, Akimoto M, Ohtsubo H, Ohtsubo E (2005) Identification and characterization of Australian wild rice strains of Oryza meridionalis and Oryza rufipogon by SINE insertion polymorphism. Genes Genet Syst 80:129–134CrossRefPubMedGoogle Scholar
  38. Zhang WK, Wang YJ, Luo GZ, Zhang JS, He CY, Wu XL, Gai JY, Chen SY (2004) QTL mapping of ten agronomic traits on the soybean (Glycine max L. Merr.) genetic map and their association with EST markers. Theor Appl Genet 108:1131–1139CrossRefPubMedGoogle Scholar
  39. Zhu YL, Song QJ, Hyten DL, Van Tassell CP, Matukumalli LK, Grimm DR, Hyatt SM, Fickus EW, Young ND, Cregan PB (2003) Single-nucleotide polymorphisms in soybean. Genetics 163:1123–1134PubMedGoogle Scholar

Copyright information

© Springer-Verlag 2010

Authors and Affiliations

  • Yongjun Shu
    • 1
  • Yong Li
    • 1
  • Yanming Zhu
    • 1
  • Zhenlei Zhu
    • 1
  • Dekang Lv
    • 1
  • Xi Bai
    • 1
  • Hua Cai
    • 1
  • Wei Ji
    • 1
  • Dianjing Guo
    • 2
  1. 1.College of Life ScienceNortheast Agricultural UniversityHarbinPeople’s Republic of China
  2. 2.State Key Laboratory of Agrobiotechnology, Department of BiologyThe Chinese University of Hong KongShatin, N.T.Hong Kong

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