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Genetic and physical mapping of new EST-derived SSRs on the A and B genome chromosomes of wheat

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Abstract

The availability of genetic maps and phenotypic data of segregating populations allows to localize and map agronomically important genes, and to identify closely associated molecular markers to be used in marker-assisted selection and positional cloning. The objective of the present work was to develop a durum wheat intervarietal genetic and physical map based on genomic microsatellite or genomic simple sequence repeats (gSSR) markers and expressed sequence tag (EST)-derived microsatellite (EST-SSR) markers. A set of 122 new EST-SSR loci amplified by 100 primer pairs was genetically mapped on the wheat A and B genome chromosomes. The whole map also comprises 149 gSSR markers amplified by 120 primer pairs used as anchor chromosome loci, two morphological markers (Black colour, Bla1, and spike glaucousness, Ws) and two seed storage protein loci (Gli-A2 and Gli-B2). The majority of SSR markers tested (182) was chromosome-specific. Out of 275 loci 241 loci assembled in 25 linkage groups assigned to the chromosomes of the A and B genome and 34 remained unlinked. A higher percentage of markers (54.4%), localized on the B genome chromosomes, in comparison to 45.6% distributed on the A genome. The whole map covered 1,605 cM. The B genome accounted for 852.2 cM of genetic distance; the A genome basic map spanned 753.1 cM with a minimum length of 46.6 cM for chromosome 5A and a maximum of 156.2 cM for chromosome 3A and an average value of 114.5 cM. The primer sets that amplified two or more loci mapped to homoeologous as well as to non-homoeologous sites. Out of 241 genetically mapped loci 213 (88.4%) were physically mapped by using the nulli-tetrasomic, ditelosomic and a stock of 58 deletion lines dividing the A and B genome chromosomes in 94 bins. No discrepancies concerning marker order were observed but the cytogenetic maps revealed in some cases small genetic distance covered large physical regions. Putative function for mapped SSRs were assigned by searching against GenBank nonredundant database using TBLASTX algorithms.

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References

  • Bandopadhyay R, Sharma S, Rustgi S, Singh R, Kumar A, Balyan HS, Gupta PK (2004) DNA polymorphism among 18 species of Triticum–Aegilops complex using wheat EST-SSRs. Plant Sci 166:349–356

    Article  CAS  Google Scholar 

  • Becker J, Heun M (1996) Barley microsatellites: allele variation and mapping. Plant Mol Biol 27:835–845

    Article  Google Scholar 

  • Blanco A, Bellomo MP, Cenci A, De Giovanni C, D’Ovidio R, Iacono E, Laddomada B, Pagnotta MA, Porceddu E, Sciancalepore A, Simeone R, Tanzarella OA (1998) A genetic linkage map of durum wheat. Theor Appl Genet 97(5–6):721–728

    Article  CAS  Google Scholar 

  • Blanco A, Simeone R, Cenci A, Gadaleta A, Tanzarella OA, Porceddu E, Salvi S, Tuberosa R, Figliuolo G, Spagnoletti P, Roder M, Korzun V (2004) Extension of the “Messapia × dicoccoides” linkage map of Triticum turgidum (L) Thell. Cell Mol Biol Lett 9(3):529–541

    PubMed  CAS  Google Scholar 

  • Brinkmann B, Klintschar M, Neuhuber F, Huhne J, Rolf B (1998) Mutation rate in human microsatellites: influence of the structure and length of the tandem repeat. Am J Hum Genet 62:1408–1415

    Article  PubMed  CAS  Google Scholar 

  • Ellegren H, Primmer CR, Sheldon BC (1995) Microsatellite “evolution”: directionality or bias? Nat Genet 11:360–362

    Article  PubMed  CAS  Google Scholar 

  • Endo TR, Gill BS (1996) The deletion stocks of common wheat. J Hered 87:295–307

    CAS  Google Scholar 

  • Eujayl I, Sorrells ME, Baum M, Wolters P, Powell W (2001) Assessment of genotypic variation among cultivated durum wheat based on EST-SSRs and genomic SSRs. Euphytica 119:39–43

    Article  CAS  Google Scholar 

  • Eujayl I, Sorrells ME, Baum M, Wolters P, Powell W (2002) Isolation of EST-derived microsatellite markers for genotyping the A and B genomes of wheat. Theor Appl Genet 104:399–407

    Article  PubMed  CAS  Google Scholar 

  • Gadaleta A, Mangini G, Mulè G, Blanco A (2007) Characterization of dinucleotide and trinucleotide EST-derived microsatellites in the wheat genome. Euphytica 153(1–2):73–85

    CAS  Google Scholar 

  • Gao LF, Jing RL, Huo NX, Li Y, Li XP, Zhou RH, Chang XP, Tang JF, Ma ZY, Jia JZ (2004) One hundred and one new microsatellite loci derived from ESTs (EST-SSRs) in bread wheat. Theor Appl Genet 108:1392–1400

    Article  PubMed  CAS  Google Scholar 

  • Goyal A, Bandopadhyay R, Sourdille P, Endo TR, Balyan HS, Gupta PK (2005) Physical molecular maps of wheat chromosomes. Funct Integr Genomics 5:260–263

    Article  PubMed  CAS  Google Scholar 

  • Gupta PK, Varshney RK, Sharma PC, Ramesh B (1999) Molecular marker and their applications in wheat breeding. Plant Breed 118:369–390

    Article  CAS  Google Scholar 

  • Gupta PK, Balyan HS, Edwards KJ, Isaac P, Korzun V, Röder M, Gautier MF, Joudrier P, Schlatter AR, Dubcovsky J, De la Pena RC, Khairallah M, Penner G, Hayden MJ, Sharp P, Keller B, Wang RCC, Hardouin JP, Jack P, Leroy P (2002) Genetic mapping of 66 new microsatellite (SSR) loci in bread wheat. Theor Appl Genet 105:413–422

    Article  PubMed  CAS  Google Scholar 

  • Guyomarc’h H, Sourdille P, Charmet G, Edwards KJ, Bernard M (2002) Characterization of polymorphic microsatellite markers from Aegilops tauschii and transferability to the D-genome of bread wheat. Theor Appl Genet 104:1164–1172

    Article  PubMed  CAS  Google Scholar 

  • Holton TA, Christopher JT, McClure L, Harker N, Henry RJ (2002) Identification and mapping of polymorphic SSR markers from expressed gene sequences of barley and wheat. Mol Breed 9:63–71

    Article  CAS  Google Scholar 

  • Joppa LR, Williams ND (1988) The Langdon durum disomic-substitutions and aneuploid analysis in tetraploid wheat. Genome 30:222–228

    Article  Google Scholar 

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

    Google Scholar 

  • La Rota M, Kantety RV, Yu JK, Sorrells ME (2005) Nonrandom distribution and frequencies of genomic and EST-derived microsatellite markers in rice, wheat, and barley. BMC Genomics 6:23–30

    Article  PubMed  CAS  Google Scholar 

  • Liu CY, Shepherd KW (1995) Inheritance of β subunits of glutenin and ϖ and γ gliadins in tetraploid wheats. Theor Appl Genet 90:1149–1157

    Article  CAS  Google Scholar 

  • Mohan A, Goyal A, Singh R, Balyan S, Gupta PK (2007) Physical mapping of wheat and rye expressed sequence tag-simple sequence repeats on wheat chromosomes. Plant Genome 1:3–13

    Article  Google Scholar 

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

    Article  PubMed  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  PubMed  CAS  Google Scholar 

  • Papi M, Sabatini S, Bouchez D, Camilleri C, Costantino P, Vittorioso P (2000) Identification and disruption of an Arabidopsis zinc finger gene controlling seed germination. Genes 14:28–33

    CAS  Google Scholar 

  • Papi M, Sabatini S, Altamura MM, Hennig L, Schafer E, Costantino P, Vittorioso P (2002) Inactivation of the phloem-specific Dof zinc finger gene DAG1 affects response to light and integrity of the testa of Arabidopsis seeds. Plant Physiol 128:411–417

    Article  PubMed  CAS  Google Scholar 

  • Peng JH, Lapitan NLV (2005) Characterization of EST-derived microsatellites in the wheat genome and development of eSSR markers. Funct Integr Genomics 5:80–96

    Article  PubMed  CAS  Google Scholar 

  • Qi LL, Echalier B, Friebe B, Gill B (2003) Molecular characterization of a set of wheat deletion stocks for use in chromosome bin mapping of ESTs. Funct Integr Genomics 3:39–55

    PubMed  CAS  Google Scholar 

  • Qi LL, Echalier B, Chao S, Lazo GR, Butler GE, Anderson OD, Akhunov ED, Dvorák J, Linkiewicz AM, Ratnasiri A, Dubcovsky J, Bermudez-Kandianis CE, Greene RA, Kantety R, La Rota MC, Munkvold JD, Sorrells SF, Sorrells ME, Dilbirligi M, Sidhu D, Erayman M, Randhawa HS, Sandhu D, Bondareva SN, Gill KS, Mahmoud A, Ma A, Miftahudin X-F, Gustafson JP, Conley EJ, Nduati V, Gonzalez-Hernandez JL, Anderson JA, Peng JH, Lapitan NLV, Hossain KG, Kalavacharla V, Kianian SF, Pathan MS, Zhang DS, Nguyen HT, Choi D-W, Fenton RD, Close TJ, McGuire PE, Qualset CO, Gill BS (2004) A chromosome bin map of 16, 000 expressed sequence tag loci and distribution of genes among the three genomes of polyploid wheat. Genetics 168:701–712

    Article  PubMed  CAS  Google Scholar 

  • Röder MS, Korzun V, Wendehake K, Plaschke J, Tixier NH, Laroy P, Ganal MV (1998) A microsatellite map of wheat. Genetics 149:2007–2023

    PubMed  Google Scholar 

  • Rudd S (2003) Expressed sequence tags: alternative or complement to whole genome sequences? Trends Plant Sci 8(7):321–329

    Article  PubMed  CAS  Google Scholar 

  • Schnable PS, Hsia AP, Nikolao BJ (1998) Genetic recombination in plants. Curr Opin Plant Biol 1(2):123–129

    Article  PubMed  CAS  Google Scholar 

  • Sears ER (1954) The aneuploids of common wheat. Univ MO Agric Exp Stn Res Bull 572:1–58

    Google Scholar 

  • Sears ER (1966) Nullisomic-tetrasomic combinations in hexaploid wheat. In: Riley R, Lewis KR (eds) Chromosome manipulations and plant genetics. Oliver and Boyd, Edinburgh, pp 20–45

    Google Scholar 

  • Sears ER, Sears LMS (1978) The telocentric chromosomes of common wheat. In: Ramanujam S (ed) Proceedings of the 5th international wheat genetics symposium. Indian Society of Genetics and Plant Breeding, New Delhi, pp 389–407

    Google Scholar 

  • Smulders MJM, Bredemeijer G, Rus-Kortekass W, Arens P, Vosman B (1997) Use of short microsatellites from database sequences to generate polymorphism among Lycopersicon esculentum cultivars and accessions of other Lycopersicon species. Theor Appl Genet 97:264–272

    Article  Google Scholar 

  • Somers DJ, Isaac P, Edwards K (2004) A high-density microsatellite consensus map for bread wheat (Triticum aestivum L). Theor Appl Genet 109:1105–1114

    Article  PubMed  CAS  Google Scholar 

  • Song QJ, Shi JR, Singh S, Fickus EW, Costa JM, Lewis J, Gill BS, Ward R, Cregan PB (2005) Development and mapping of microsatellite (SSR) markers in wheat. Theor Appl Genet 110:550–560

    Article  PubMed  CAS  Google Scholar 

  • Sourdille P, Tavaud M, Charmet G, Bernard M (2001) Transferability of wheat microsatellites to diploid Triticeae species carrying the A, B and D genomes. Theor Appl Genet 103:346–352

    Article  CAS  Google Scholar 

  • Sourdille P, Cadalen T, Guyomarc’h H, Snape JW, Perretant MR, Charmet G, Boeuf C, Bernard S, Bernard M (2003) An update of the Courtot × Chinese Spring intervarietal molecular marker linkage map for the QTL detection of agronomic traits in wheat. Theor Appl Genet 106:530–538

    PubMed  CAS  Google Scholar 

  • Sourdille P, Sukhwinder S, Cadalen T, Brown-Guedira GL, Gay G, Qi L, Gill BS, Dufour P, Murigneux A, Bernard M (2004) Microsatellite-based deletion bin system for the establishment of genetic-physical map relationships in wheat (Triticum aestivum L). Funct Integr Genomics 4:12–25

    Article  PubMed  CAS  Google Scholar 

  • Van Ooijen JW, Voorrips RE (2001) JoinMap 3, software in the calculation of genetic linkage maps. Plant Research International, Wageningen. http://www.Kyazmanl/index,php/mcJoinMap

  • Weising K, Fing RWM, Keeling RG, Atkinson RG, Gardner RC (1996) Characterization of microsatellites from Actinidia chinensis. Mol Breed 2:117–131

    Article  CAS  Google Scholar 

  • Wierdl M, Dominska M, Peters TD (1997) Microsatellite instability in yeast: dependence on the length of the microsatellite. Genetics 146:769–779

    PubMed  CAS  Google Scholar 

  • Xue SL, Zhang ZZ, Lin F, Kong Z, Cao Y, Li C, Yi H, Mei M, Zhu H, Wu J, Xu H, Zhao D, Tian D, Zhang C, Ma Z (2008) A high-density intervarietal map of the wheat genome enriched with markers derived from expressed sequence tags. Theor Appl Genet 117:181–189

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

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Acknowledgements

This research was supported by a grant from the Ministero delle Politiche Agricole, project ‘FRUMISIS’, and Ministero dell’Università e della Ricerca, Italy, project ‘AGROGEN’.

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  1. Department of Agro-Forestry and Environmental Biology and Chemistry, University of Bari, Via Amendola 165/A, 70126, Bari, Italy

    A. Gadaleta, A. Giancaspro, S. L. Giove, S. Zacheo, G. Mangini, R. Simeone, A. Signorile & A. Blanco

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  1. A. Gadaleta
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  2. A. Giancaspro
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  7. A. Signorile
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  8. A. Blanco
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Correspondence to A. Blanco.

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Communicated by P. Langridge.

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Gadaleta, A., Giancaspro, A., Giove, S.L. et al. Genetic and physical mapping of new EST-derived SSRs on the A and B genome chromosomes of wheat. Theor Appl Genet 118, 1015–1025 (2009). https://doi.org/10.1007/s00122-008-0958-1

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  • DOI: https://doi.org/10.1007/s00122-008-0958-1

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