Skip to main content

Advertisement

SpringerLink
Log in

SNP discovery and genetic mapping of T-DNA insertional mutants in Fragaria vesca L.

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

Abstract

As part of a program to develop forward and reverse genetics platforms in the diploid strawberry [Fragaria vesca L.; (2n = 2x = 14)] we have generated insertional mutant lines by T-DNA mutagenesis using pCAMBIA vectors. To characterize the T-DNA insertion sites of a population of 108 unique single copy mutants, we utilized thermal asymmetric interlaced PCR (hiTAIL-PCR) to amplify the flanking region surrounding either the left or right border of the T-DNA. Bioinformatics analysis of flanking sequences revealed little preference for insertion site with regard to G/C content; left borders tended to retain more of the plasmid backbone than right borders. Primers were developed from F. vesca flanking sequences to attempt to amplify products from both parents of the reference F. vesca 815 × F. bucharica 601 mapping population. Polymorphism occurred as: presence/absence of an amplification product for 16 primer pairs and different size products for 12 primer pairs, For 46 mutants, where polymorphism was not found by PCR, the amplification products were sequenced to reveal SNP polymorphism. A cleaved amplified polymorphic sequence/derived cleaved amplified polymorphism sequence (CAPS/dCAPS) strategy was then applied to find restriction endonuclease recognition sites in one of the parental lines to map the SNP position of 74 of the T-DNA insertion lines. BLAST search of flanking regions against GenBank revealed that 46 of 108 flanking sequences were close to presumed strawberry genes related to annotated genes from other plants.

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

Access this article

Log in via an institution

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

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6

Similar content being viewed by others

References

  • Aggarwal RK, Hendre PS, Varshney RK, Bhat PR, Krishnakumar V, Lalji S (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 

  • Altschul SF, Madden TL, Schaffer AA, Zhang JH, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402

    Article  CAS  PubMed  Google Scholar 

  • Brookes AJ (1999) The essence of SNPs. Gene 234:177–186

    Article  CAS  PubMed  Google Scholar 

  • Brunaud V, Balzergue S, Dubreucq B, Aubourg S, Samson F, Chauvin S, Bechtold N, Cruaud C, DeRose R, Pelletier G, Lepiniec L, Caboche M, Lecharny A (2002) T-DNA integration into the Arabidopsis genome depends on sequences of pre-insertion sites. EMBO Rep 3:1152–1157

    Article  CAS  PubMed  Google Scholar 

  • Bundock PC, Henry RJ (2004) Single nucleotide polymorphism, haplotype diversity and recombination in the Isa gene of barley. Theor Appl Genet 109:543–551

    Article  CAS  PubMed  Google Scholar 

  • Conn HJ (1942) Validity of the genus Alcaligenes. J Bacteriol 44:353–360

    CAS  PubMed  Google Scholar 

  • Dafny-Yelin M, Tovkach A, Tzfira T (2009) Integration of Agrobacterium T-DNA in plant cells. In: Meier I (ed) Functional organization of the plant nucleus. Springer, Berlin, pp 157–186

    Chapter  Google Scholar 

  • Délye C, Boucansaud K, Pernin F, Le Corre V (2009) Variation in the gene encoding acetolactate-synthase in Lolium species and proactive detection of mutant, herbicide-resistant alleles. Weed Res 49:326–336

    Article  Google Scholar 

  • Folta KM, Davis TM (2006) Strawberry genes and genomics. Crit Rev Plant Sci 25:399–415

    Article  CAS  Google Scholar 

  • Hadonou AM, Sargent DJ, Wilson F, James CM, Simpson DW (2004) Development of microsatellite markers in Fragaria, their use in genetic diversity analysis, and their potential for genetic linkage mapping. Genome 47:429–438

    Article  CAS  PubMed  Google Scholar 

  • Henry RJ (2008) Future prospects for plant genotyping. In: Henry RJ (ed) Plant genotyping II: SNP technology. CABI, Wallingford, pp 272–280

    Chapter  Google Scholar 

  • Hiei Y, Ohta S, Komari T, Kumashiro T (1994) Efficient transformation of rice (Oryza sativa L.) mediated by Agrobacterium and sequence analysis of the boundaries of the T-DNA. Plant J 6:271–282

    Article  CAS  PubMed  Google Scholar 

  • Jing R, Johnson R, Seres A, Kiss G, Ambrose MJ, Knox MR, Ellis THN, Flavell AJ (2007) Gene-based sequence diversity analysis of field pea (Pisum). Genetics 177:2263–2275

    Article  CAS  PubMed  Google Scholar 

  • Knox MR, Ellis THN (2002) Excess heterozygosity contributes to genetic map expansion in pea recombinant inbred populations. Genetics 162:861–873

    CAS  PubMed  Google Scholar 

  • Kolesnik T, Szeverenyi I, Bachmann D, Kumar CS, Jiang S, Ramamoorthy R, Cai M, Ma ZG, Sundaresan V, Ramachandran S (2004) Establishing an efficient Ac/Ds tagging system in rice: large-scale analysis of Ds flanking sequences. Plant J 37:301–314

    CAS  PubMed  Google Scholar 

  • Komori T, Nitta N (2005) Utilization of the CAPS/dCAPS method to convert rice SNPs into PCR-based markers. Breed Sci 55:93–98

    Article  CAS  Google Scholar 

  • Konieczny A, Ausubel FM (1993) A procedure for mapping Arabidopsis mutations using co-dominant ecotype-specific PCR-based markers. Plant J 4:403–410

    Article  CAS  PubMed  Google Scholar 

  • Krysan PJ, Young JC, Sussman MR (1999) T-DNA as an insertional mutagen in Arabidopsis. Plant Cell 11:2283–2290

    Article  CAS  PubMed  Google Scholar 

  • Lai Z, Livingstone K, Zou Y, Church SA, Knapp SJ, Andrews J, Rieseberg LH (2005) Identification and mapping of SNPs from ESTs in sunflower. Theor Appl Genet 111:1532–1544

    Article  CAS  PubMed  Google Scholar 

  • Li Y, Rosso MG, Ülker B, Weisshaar B (2006) Analysis of T-DNA insertion site distribution patterns in Arabidopsis thaliana reveals special features of genes without insertions. Genomics 87:645–652

    Article  CAS  PubMed  Google Scholar 

  • Liu Y (2005) Construction of a genetic map and location of quantitative trait loci for number of flowers per truss traits in tomato by SSR markers. J Nanjing Agric Univ 28:30–34

    Google Scholar 

  • Liu YG, Chen Y (2007) High-efficiency thermal asymmetric interlaced PCR for amplification of unknown flanking sequences. BioTechniques 43:649–656

    Article  CAS  PubMed  Google Scholar 

  • Liu Y-G, Whittier RF (1995) Thermal asymmetric interlaced PCR: automatable amplification and sequencing of insert end fragments from P1 and YAC clones for chromosome walking. Genomics 25:674–681

    Article  CAS  PubMed  Google Scholar 

  • Michaels SD, Amasino RM (1998) A robust method for detecting single-nucleotide changes as polymorphic markers by PCR. Plant J 14:381–385

    Article  CAS  PubMed  Google Scholar 

  • Muehlbauer FJ, Rajesh PN (2008) Chickpea, a common source of protein and starch in the semi-arid tropics. In: Jorgensen RA (ed) Plant genetics and genomics: crops and models. Springer, Heidelberg, pp 171–186

    Google Scholar 

  • Murai H, Sharma PN, Murata K, Hashimoto Z, Ketipearachi Y, Shimizu T, Takumi S, Mori N, Kawasaki S, Nakamura C (2003) Constructing linkage maps of brown planthopper resistance genes Bph1, bph2, and Bph9 on rice chromosome 12. In: Khush GS, Brar DS, Hardy B (eds) Rice genetics collection. World Scientific Publishing, Singapore, pp 263–265

    Google Scholar 

  • Neff MM, Neff JD, Chory J, Pepper AE (1998) dCAPS, a simple technique for the genetic analysis of single nucleotide polymorphisms: experimental applications in Arabidopsis thaliana genetics. Plant J 14:387–392

    Article  CAS  PubMed  Google Scholar 

  • Neff MM, Turk E, Kalishman M (2002) Web-based primer design for single nucleotide polymorphism analysis. Trends Genet 18:613–615

    Article  CAS  PubMed  Google Scholar 

  • Olmstead JW (2008) Construction of an intra-specific sweet cherry (Prunus avium L.) genetic linkage map and synteny analysis with the Prunus reference map. Tree Genet Genom 4:897–910

    Article  Google Scholar 

  • Oosumi T, Gruszewski HA, Blischak LA, Baxter AJ, Wadl PA, Shuman JL, Veilleux RE, Shulaev V (2006) High-efficiency transformation of the diploid strawberry (Fragaria vesca) for functional genomics. Planta 223:1219–1230

    Article  CAS  PubMed  Google Scholar 

  • Pan XK, Li Y, Stein L (2005) Site preferences of insertional mutagenesis agents in Arabidopsis. Plant Physiol 137:168–175

    Article  CAS  PubMed  Google Scholar 

  • Potter D, Luby JJ, Harrison RE (2000) Phylogenetic relationships among species of Fragaria (Rosaceae) inferred from non-coding nuclear and chloroplast DNA sequences. Syst Bot 25:337–348

    Article  Google Scholar 

  • Robinson SJ, Tang LH, Mooney BAG, McKay SJ, Clarke WE, Links MG, Karcz S, Regan S, Wu YY, Gruber MY, Cui DJ, Yu M, Parkin IAP (2009) An archived activation tagged population of Arabidopsis thaliana to facilitate forward genetics approaches. BMC Plant Biol 9:101

    Article  PubMed  Google Scholar 

  • Rousseau-Gueutin M, Lerceteau-Köhler E, Barrot L, Sargent DJ, Monfort A, Simpson D, Arús P, Guérin G, Denoyes-Rothan B (2008) Comparative genetic mapping between octoploid and diploid Fragaria species reveals a high level of colinearity between their genomes and the essentially disomic behavior of the cultivated octoploid strawberry. Genetics 179:2045–2060

    Article  PubMed  Google Scholar 

  • Sargent DJ, Hadonou AM, Simpson DW (2003) Development and characterization of polymorphic microsatellite markers from Fragaria viridis, a wild diploid strawberry. Mol Ecol Notes 3:550–552

    Article  CAS  Google Scholar 

  • Sargent DJ, Davis TM, Tobutt KR, Wilkinson MJ, Battey NH, Simpson DW (2004) A genetic linkage map of microsatellite, gene-specific and morphological markers in diploid Fragaria. Theor Appl Genet 109:1385–1391

    Article  CAS  PubMed  Google Scholar 

  • Sargent DJ, Clarke J, Simpson DW, Tobutt KR, Arus P, Monfort A, Vilanova S, Denoyes-Rothan B, Rousseau M, Folta KM, Bassil NV, Battey NH (2006) An enhanced microsatellite map of diploid Fragaria. Theor Appl Genet 112:1349–1359

    Article  CAS  PubMed  Google Scholar 

  • Sargent DJ, Rys A, Nier S, Simpson DW, Tobutt KR (2007) The development and mapping of functional markers in Fragaria and their transferability and potential for mapping in other genera. Theor Appl Genet 114:373–384

    Article  CAS  PubMed  Google Scholar 

  • Sargent DJ, Cipriani G, Vilanova S, Gil-Ariza D, Arús P, Simpson DW, Tobutt KR, Monfort A (2008) The development of a bin mapping population and the selective mapping of 103 markers in the diploid Fragaria reference map. Genome 51:120–127

    Article  CAS  PubMed  Google Scholar 

  • Sargent DJ, Marchese A, Simpson DW, Howad W, Fernández-Fernández F, Monfort A, Arús P, Evans KM, Tobutt KR (2009) Development of “universal” gene-specific markers from Malus spp. cDNA sequences, their mapping and use in synteny studies within Rosaceae. Tree Genet Genom 5:133–145

    Article  Google Scholar 

  • Shuangyan C, Weizheng J, Mingyi W, Fan Z, Jie Z, Qiaojun J, Yunrong W, Feiyan L, Ping W (2003) Distribution and characterization of over 1000 T-DNA tags in rice genome. Plant J 36:105–113

    Article  Google Scholar 

  • Shulaev V, Korban SS, Sosinski B, Abbott AG, Aldwinckle HS, Folta KM, Iezzoni A, Main D, Arús P, Dandekar AM, Lewers K, Brown SK, Davis TM, Gardiner SE, Potter D, Veilleux RE (2008) Multiple models for Rosaceae genomics. Plant Physiol 147:985–1003

    Article  CAS  PubMed  Google Scholar 

  • Smith EF, Townsend CO (1907) A plant tumor of bacterial origin. Science 25:671–673

    Article  CAS  PubMed  Google Scholar 

  • Tanhuanpää P, Kalendar R, Schulman AH, Kiviharju E (2008) The first doubled haploid linkage map for cultivated oat. Genome 51:560–569

    Article  PubMed  Google Scholar 

  • Upadhyaya NM, Zhu QH, Zhou XR, Eamens AL, Hoque MS, Ramm K, Shivakkumar R, Smith KF, Pan ST, Li SZ, Peng KF, Kim SJ, Dennis ES (2006) Dissociation (Ds) constructs, mapped Ds launch pads and a transiently-expressed transposase system suitable for localized insertional mutagenesis in rice. Theor Appl Genet 112:1326–1341

    Article  CAS  PubMed  Google Scholar 

  • Van Ooijen JW, Voorrips R (2001) Joinmap 3.0: software for the calculation of genetic linkage maps. Plant Research International, Wageningen

    Google Scholar 

  • Voorrips RE (2002) MapChart: software for the graphical presentation of linkage maps and QTLs. J Hered 93:77–78

    Article  CAS  PubMed  Google Scholar 

  • Windels P, De Buck S, Depicker A (2008) Agrobacterium tumefaciens-mediated transformation: Patterns of T-DNA integration into the host genome. In: Tzfira T, Citovsky V (eds) Agrobacterium: from biology to biotechnology. Springer, New York, pp 441–481

    Chapter  Google Scholar 

  • Woody ST, Austin-Phillips S, Amasino RM, Krysan PJ (2007) The WiscDsLox T-DNA collection: an Arabidopsis community resource generated by using an improved high-throughput T-DNA sequencing pipeline. J Plant Res 120:157–165

    Article  CAS  PubMed  Google Scholar 

  • Yanagisawa T, Kiribuchi-Otobe C, Hirano H, Suzuki Y, Fujita M (2003) Detection of single nucleotide polymorphism (SNP) controlling the waxy character in wheat by using a derived cleaved amplified polymorphic sequence (dCAPS) marker. Theor Appl Genet 107:84–88

    CAS  PubMed  Google Scholar 

  • Zambryski P, Depicker A, Kruger K, Goodman HM (1982) Tumour induction by Agrobacterium tumefaciens: analysis of the boundaries of T-DNA. J Mol Appl Genet 1:361–370

    CAS  PubMed  Google Scholar 

  • Zhao B, Deng Q-M, Zhang Q-J, Li J-Q, Ye S-P, Liang Y-S, Peng Y, Li P (2006a) Analysis of segregation distortion of molecular markers in F2 population of rice. Acta Genet Sin 33:449–457

    Article  CAS  PubMed  Google Scholar 

  • Zhao T, Palotta M, Langridge P, Prasad M, Graner A, Schulze-Lefert P, Koprek T (2006b) Mapped Ds/T-DNA launch pads for functional genomics in barley. Plant J 47:811–826

    Article  PubMed  Google Scholar 

Download references

Acknowledgments

This work was supported by the USDA/NRI 2008-02284, Hatch VA-135816, the East Malling Trust for Horticulture Research, the BBSRC, and a Virginia Tech ASPIRES Grant.

Author information

Authors and Affiliations

  1. Department of Horticulture, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA

    J. J. Ruiz-Rojas, V. Shulaev, S. H. Holt & Richard E. Veilleux

  2. East Malling Research (EMR), New Road, East Malling, Kent, ME19 6BJ, UK

    D. J. Sargent & A. Ciordia

  3. Department of Horticultural Science, North Carolina State University, 600 Laureate Way, Kannapolis, NC, 28081, USA

    J. Pattison

  4. Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA

    V. Shulaev & A. W. Dickerman

Authors
  1. J. J. Ruiz-Rojas
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. D. J. Sargent
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. V. Shulaev
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. A. W. Dickerman
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. J. Pattison
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. S. H. Holt
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. A. Ciordia
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Richard E. Veilleux
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Richard E. Veilleux.

Additional information

Communicated by A. Schulman.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary Tables (DOC 78 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Ruiz-Rojas, J.J., Sargent, D.J., Shulaev, V. et al. SNP discovery and genetic mapping of T-DNA insertional mutants in Fragaria vesca L.. Theor Appl Genet 121, 449–463 (2010). https://doi.org/10.1007/s00122-010-1322-9

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00122-010-1322-9

Keywords

Search

Navigation