Skip to main content
SpringerLink
Log in

An integrated DArT-SSR linkage map of durum wheat

  • Published:
Molecular Breeding Aims and scope Submit manuscript

Abstract

Genetic mapping in durum wheat (Triticum durum Desf.) is constrained by its large genome and allopolyploid nature. We developed a Diversity Arrays Technology (DArT) platform for durum wheat to enable efficient and cost-effective mapping and molecular breeding applications. Genomic representations from 56 durum accessions were used to assemble a DArT genotyping microarray. Microsatellite (SSR) and DArT markers were mapped on a durum wheat recombinant inbred population (176 lines). The integrated DArT-SSR map included 554 loci (162 SSRs and 392 DArT markers) and spanned 2022 cM (5 cM/marker on average). The DArT markers from durum wheat were positioned in respect to anchor SSRs and hexaploid wheat DArT markers. DArT markers compared favourably to SSRs to evaluate genetic relationships among the durum panel, with 1315 DArT polymorphisms found across the accessions. Combining DArT and SSR platforms provides an efficient and rapid method of generating linkage maps in durum wheat.

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

Similar content being viewed by others

Abbreviations

DArT:

Diversity arrays technology

chr:

Chromosome

cv:

Cultivar

‘C × L’:

Colosseo × Lloyd

ITMI map:

Ta-Synthetic/Opata-BARC map (Song et al. 2005)

‘K × S’:

Kofa × Svevo

PCR:

Polymerase chain reaction

RIL:

Recombinant inbred line

SSR:

Simple sequence repeat or microsatellite marker

References

  • Akbari M, Wenzl P, Caig V, Carling J, Xia L, Yang S et al (2006) Diversity arrays technology (DArT) for high-throughput profing of the hexaploid wheat genome. Theor Appl Genet 113:1409–1420. doi:10.1007/s00122-006-0365-4

    Article  PubMed  CAS  Google Scholar 

  • Balfourier F, Roussel V, Strelchenko P, Exbrayat-Vinson F, Sourdille P, Boutet G et al (2007) A worldwide bread wheat core collection arrayed in a 384-well plate. Theor Appl Genet 114:1265–1275. doi:10.1007/s00122-007-0517-1

    Article  PubMed  Google Scholar 

  • Bassam BJ, Anollés GC, Gresshoff P (1991) Fast and sensitive silver staining of DNA in polyacrylamide gels. Anal Biochem 196:80–83. doi:10.1016/0003-2697(91)90120-I

    Article  PubMed  CAS  Google Scholar 

  • Blanco A, Bellomo MP, Cenci A, De Giovanni C, D’Ovidio R, Iacono E et al (1998) A genetic linkage map of durum wheat. Theor Appl Genet 97:721–728. doi:10.1007/s001220050948

    Article  CAS  Google Scholar 

  • Breseghello F, Sorrells ME (2006) Association mapping of kernel size and milling quality in wheat (Triticum aestivum L.) cultivars. Genetics 172:1165–1177. doi:10.1534/genetics.105.044586

    Article  PubMed  Google Scholar 

  • Cadalen T, Boeuf C, Bernard S, Bernard M (1997) An intervarietal molecular marker map in Triticum aestivum L. Em. Thell. and comparison with a map from a wide cross. Theor Appl Genet 94:367–377. doi:10.1007/s001220050425

    Article  CAS  Google Scholar 

  • Crossa J, Burgueño J, Dreisigacker S, Vargas M, Herrera-Foessel SA, Lillemo M et al (2007) Association analysis of historical bread wheat germplasm using additive genetic covariance of relatives and population structure. Genetics 177:1889–1913. doi:10.1534/genetics.107.078659

    Article  PubMed  CAS  Google Scholar 

  • Esch E, Szymaniak JM, Yates H, Pawlowski WP, Bucler ES (2007) Using crossover breakpoints in recombinant inbred lines to identify quantitative trait loci controlling the global recombination frequency. Genetics published ahead of print doi:10.1534/genetics.107.080622

  • 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 

  • Faris JD, Haen KM, Gill BS (2000) Saturation mapping of a gene-rich recombination hot spot region in wheat. Genetics 154:823–835

    PubMed  CAS  Google Scholar 

  • Faure S, Noyer JL, Horry JP, Bakry F, Lanaud C, Gonzalez de Leon D (1993) A molecular marker-based linkage map of diploid bananas (Musa acuminata). Theor Appl Genet 87:517–526. doi:10.1007/BF00215098

    Article  CAS  Google Scholar 

  • Foolad MR, Arulsekar S, Becerra V, Bliss FA (1995) A genetic map of Prunus based on an interspecific cross between peach and almond. Theor Appl Genet 91:262–269. doi:10.1007/BF00220887

    Article  CAS  Google Scholar 

  • Gill KS, Gill BS, Endo TR, Boyko EV (1996a) Identification of high-density mapping of gene-rich regions in chromosome group 5 of wheat. Genetics 143:1001–1012

    PubMed  CAS  Google Scholar 

  • Gill KS, Gill BS, Endo TR, Taylor T (1996b) Identification and high-density mapping of gene-rich regions in chromosome group 1 of wheat. Genetics 144:1883–1891

    PubMed  CAS  Google Scholar 

  • Giunta F, Motzo R, Pruneddu G (2007) Trends since 1900 in the yield potential of Italian-bred durum wheat cultivars. Eur J Agron 27:12–24. doi:10.1016/j.eja.2007.01.009

    Article  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. doi:10.1007/s10142-005-0146-1

    Article  PubMed  CAS  Google Scholar 

  • Gupta PK, Balyan HS, Edwards KJ, Isaac P, Korzun V, Roder 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, Edwards KJ, Bernard M (2002) Studies of the transferability of microsatellites derived from Triticum tauschii to hexaploid wheat and to diploid related species using amplification, hybridization and sequence comparisons. Theor Appl Genet 105:736–744

    Article  PubMed  CAS  Google Scholar 

  • Hayden MJ, Nguyen TM, Waterman A, McMichael GL, Chalmers KJ (2008) Application of multiplex-ready PCR for fluorescence-based SSR genotyping in barley and wheat. Mol Breed. doi:10.1007/s11032-007-9127-5

  • Jaccoud D, Peng K, Feinstein D, Kilian A (2001) Diversity arrays: a solid state technology for sequence information independent genotyping. Nucleic Acids Res 29:E25. doi:10.1093/nar/29.4.e25

    Article  PubMed  CAS  Google Scholar 

  • Kilian A, Huttner E, Wenzl P, Jaccoud D, Carling J, Caig V et al (2005) The fast and the cheap: SNP and DArT-based whole genome profiling for crop improvement. In: Tuberosa R, Phillips RL, Gale M (eds) Proceedings of the international congress in the wake of the double helix: from the green revolution to the gene revolution. Avenue Media, Bologna, Italy, 27–31 May 2003, pp 443–461

  • Koebner RM, Summers RW (2003) 21st century wheat breeding: plot selection or plate detection? Trends Biotechnol 21:59–63. doi:10.1016/S0167-7799(02)00036-7

    Article  PubMed  CAS  Google Scholar 

  • Korzun V, Röder MS, Wendekake K, Pasqualone A, Lotti C, Ganal MW et al (1999) Integration of dinucleotide microsatellites from hexaploid bread wheat into a genetic linkage map of durum wheat. Theor Appl Genet 98:1202–1207. doi:10.1007/s001220051185

    Article  CAS  Google Scholar 

  • Langridge P (2005) Molecular breeding of wheat and barley. In: Tuberosa R, Phillips RL, Gale M (eds) Proceedings of the international congress in the wake of the double helix: from the green revolution to the gene revolution. Avenue Media, Bologna, Italy, 27–31 May 2003, pp 279–286

  • Langridge P, Chalmers K (1998) Techniques for marker development. In: Proceedings of the 9th international wheat genet symposium, vol 1. Saskatchewan, Canada, pp 107–117

  • Lincoln SE, Lander ES (1992) Systematic detection of errors in genetic linkage data. Genomics 14:604–610. doi:10.1016/S0888-7543(05)80158-2

    Article  PubMed  CAS  Google Scholar 

  • Linkiewicz AM, Qi LL, Gill BS, Ratnasiri A, Echalier B, Chao S et al (2004) A 2500-locus bin map of wheat homoeologous group 5 provides insights on gene distribution and colinearity with rice. Genetics 168:665–676. doi:10.1534/genetics.104.034835

    Article  PubMed  CAS  Google Scholar 

  • Lu H, Romero-Severson J, Bernardo R (2002) Chromosomal regions associated with segregation distortion in maize. Theor Appl Genet 105:622–628. doi:10.1007/s00122-002-0970-9

    Article  PubMed  CAS  Google Scholar 

  • Maccaferri M, Sanguineti MC, Donini P, Tuberosa R (2003) Microsatellite analysis reveals a progressive widening of the genetic basis in the elite durum wheat germplasm. Theor Appl Genet 107:783–797. doi:10.1007/s00122-003-1319-8

    Article  PubMed  CAS  Google Scholar 

  • Maccaferri M, Sanguineti MC, Noli E, Tuberosa R (2005) Population structure and long-range linkage disequilibrium in a durum wheat elite collection. Mol Breed 15:271–290. doi:10.1007/s11032-004-7012-z

    Article  CAS  Google Scholar 

  • Maccaferri M, Sanguineti MC, Natoli V, Ortega JAL, Salem MB, Bort J et al (2006) A panel of elite accessions of durum wheat (Triticum durum Desf.) suitable for association mapping studies. Plant Genet Resour 4:79–85

    Article  CAS  Google Scholar 

  • Maccaferri M, Stefanelli S, Rotondo F, Tuberosa R, Sanguineti MC (2007) Relationships among durum wheat accessions. I. Comparative analysis of SSR, AFLP, and phenotypic data. Genome 50:373–384. doi:10.1139/G06-151

    Article  PubMed  CAS  Google Scholar 

  • Maccaferri M, Sanguineti MC, Corneti S, Jose LAO, Ben Salern M, Bort J et al (2008) Quantitative trait loci for grain yield and adaptation of durum wheat (Triticum durum Desf.) across a wide range of water availability. Genetics 178:489–511. doi:10.1534/genetics.107.077297

    Article  PubMed  Google Scholar 

  • Mantel NA (1967) The detection of disease clustering and a generalized regression approach. Cancer Res 27:209–220

    PubMed  CAS  Google Scholar 

  • Mantovani P, van der Linden G, Maccaferri M, Sanguineti MC, Tuberosa R (2006) Nucleotide-binding site (NBS) profiling of genetic diversity in durum wheat. Genome 49:1473–1480. doi:10.1139/G06-100

    Article  PubMed  CAS  Google Scholar 

  • Nachit MM, Elouafi I, Pagnotta MA, El Saleh A, Iacono E, Labhilili M et al (2001) Molecular linkage map for an intraspecific recombinant inbred population of durum wheat (Triticum turgidum L. var. durum). Theor Appl Genet 102:177–186. doi:10.1007/s001220051633

    Article  CAS  Google Scholar 

  • Paillard S, Schnurbusch T, Winzeler M, Messmer M, Sourdille P, Abderhalden O, Keller B, Schachermayr G (2003) An integrative genetic linkage map of winter wheat (Triticum aestivum L.). Theor Appl Genet 107:1235–1242

    Article  PubMed  CAS  Google Scholar 

  • Peng J, Korol AB, Fahima T, Röder MS, Ronin YI, Li YC et al (2000) Molecular genetic maps in wild emmer wheat, Triticum dicoccoides: genome-wide coverage, massive negative interference, and putative quasi-linkage. Genome Res 10:1509–1531. doi:10.1101/gr.150300

    Article  PubMed  CAS  Google Scholar 

  • Perrier X, Flori A, Bonnot F (2003) Data analysis methods. In: Hamon P, Seguin M, Perrier X, Glaszmann JC (eds) Genetic diversity of cultivated tropical plants. Enfield, Science Publishers, Montpellier, pp 43–76

    Google Scholar 

  • Perrier X, Jacquemoud-Collet JP (2006) DARwin software (http://darwin cirad fr/darwin)

  • Plaschke J, Ganal MW, Röder MS (1995) Detection of genetic diversity in closely related bread wheat using microsatellite markers. Theor Appl Genet 92:1078–1084

    Google Scholar 

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

    PubMed  Google Scholar 

  • Saghai-Maroof MA, Soliman KM, Jorgensen RA, Allard RW (1984) Ribosomal DNA sepacer-length polymorphism in barley: Mendelian inheritance, chromosomal location, and population dynamics. Proc Natl Acad Sci USA 81:8014–8019. doi:10.1073/pnas.81.24.8014

    Article  PubMed  CAS  Google Scholar 

  • Sandhu D, Champoux JA, Bondareva SN, Gill KS (2001) Identification and physical localization of useful genes and markers to major gee-rich region on wheat group 1S chromosomes. Genetics 157:1735–1747

    PubMed  CAS  Google Scholar 

  • Sanguineti MC, Li S, Maccaferri M, Corneti S, Rotondo F, Chiari T et al (2007) Genetic dissection of seminal root architecture in elite durum wheat germplasm. Ann Appl Biol 151:291–305. doi:10.1111/j.1744-7348.2007.00198.x

    Article  Google Scholar 

  • Semagn K, Bjornstad A, Skinnes H, Maroy AG, Tarkegne Y, William M (2006) Distribution of DArT, AFLP, and SSR markers in a genetic linkage map of a doubled-haploid hexaploid wheat population. Genome 49:545–555. doi:10.1139/G06-002

    Article  PubMed  CAS  Google Scholar 

  • Singh K, Ghai M, Garg M, Chhuneja P, Kaur P, Schnurbusch T, Keller B, Dhaliwal HS (2007) An integrated molecular linkage map of diploid wheat based on a Triticum boeoticum x T. monococcum RIL population. Theor Appl Genet 115:301–312

    Article  PubMed  CAS  Google Scholar 

  • Somers DJ, Kirkpatrick R, Moniwa M, Walsh A (2003) Mining single-nucleotide polymorphisms from hexaploid wheat ESTs. Genome 46:431–437. doi:10.1139/g03-027

    Article  PubMed  CAS  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. doi:10.1007/s00122-004-1740-7

    Article  PubMed  CAS  Google Scholar 

  • Song QJ, Fickus EW, Cregan PB (2002) Characterization of trinucleotide SSR motifs in wheat. Theor Appl Genet 104:286–293

    Article  PubMed  CAS  Google Scholar 

  • Song QJ, Shi JR, Singh S, Fickus EW, Costa JM, Lewis J et al (2005) Development and mapping of microsatellite (SSR) markers in wheat. Theor Appl Genet 110:550–560. doi:10.1007/s00122-004-1871-x

    Article  PubMed  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, Singh S, Cadalen T, Brown-Guedira G, Gay G, Qi L et al (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. doi:10.1007/s10142-004-0106-1

    Article  PubMed  CAS  Google Scholar 

  • Stam P (1993) Construction of integrated genetic linkage maps by means of a new computer package: JoinMap. Plant J 3:739–744

    Article  CAS  Google Scholar 

  • Tivang JG, Nienhuis J, Smith OS (1994) Estimation of sampling variance of molecular marker data using the bootstrap procedure. Theor Appl Genet 89:259–264. doi:10.1007/BF00225151

    Article  Google Scholar 

  • Torada A, Koike M, Mochida K, Ogihara Y (2006) SSR-based linkage map with new markers using an intraspecific population of common wheat. Theor Appl Genet 112:1042–1051. doi:10.1007/s00122-006-0206-5

    Article  PubMed  CAS  Google Scholar 

  • van Ooijen JW (2006) JoinMap 4, software for the calculation of genetic linkage maps in experimental populations. Kyazma BV, Wageningen, Netherlands

    Google Scholar 

  • van Os H, Stam P, Visser RGF, van Eck HJ (2005) RECORD: a novel method for ordering loci on a genetic linkage map. Theor Appl Genet 112:30–40. doi:10.1007/s00122-005-0097-x

    Article  PubMed  CAS  Google Scholar 

  • van Os H, Andrzejewski S, Bakker E, Barrena I, Bryan GJ, Caromel B, Ghareeb B, Isidore E, de Jong W, van Koert P, Lefebvre V, Milbourne D, Ritter E, Rouppe van der Voort JNAM, Rousselle-Bourgeois F, van Vliet J, Waugh R, Visser RGF, Bakker J, van Eck HJ (2006) Construction of a 10, 000-marker ultradense genetic recombination map of potato: providing a framework for accelerated gene isolation and a genomewide physical map. Genetics 173:1075–1087. doi:10.1534/genetics.106.055871

    Article  PubMed  CAS  Google Scholar 

  • Varshney RK, Tuberosa R (2007) Genomics-assisted crop improvement: an overview. In: Varshney RK, Tuberosa R (eds) Genomics-assisted crop improvement, vol 1: genomics approaches and platforms. Springer, Dordrecht, The Netherlands, pp 1–12

    Chapter  Google Scholar 

  • Weir BS, Anderson AD, Hepler AB (2006) Genetic relatedness analysis: modern data and new challenges. Nat Rev Genet 7:771–780. doi:10.1038/nrg1960

    Article  PubMed  CAS  Google Scholar 

  • Wenzl P, Carling J, Kudrna D, Jaccoud D, Huttner E, Kleinhofs A et al (2004) Diversity arrays technology (DArT) for whole-genome profiling of barley. Proc Natl Acad Sci USA 101:9915–9920. doi:10.1073/pnas.0401076101

    Article  PubMed  CAS  Google Scholar 

  • Wenzl P, Li H, Carling J, Zhou M, Raman H, Paul E et al (2006) A high-density consensus map of barley linking DArT markers to SSR, RFLP, and STS loci and agricultural traits. BMC Genomics 7:206. doi:10.1186/1471-2164-7-206

    Article  PubMed  CAS  Google Scholar 

  • Williams RW, Gu J, Qi S, Lu L (2001) The genetic structure of recombinant inbred mice: high-resolution consensus maps for complex trait analysis. Genome Biol 2:research0046.1-0046.18

  • Xu Y, Zhu L, Xiao J, Huang N, McCouch SR (1997) Chromosomal regions associated with segregation distortion of molecular markers in F2, backcross, doubled haploid, and recombinant inbred populations in rice (Oryza sativa L.). Mol Gen Genet 253:535–545. doi:10.1007/s004380050355

    Article  PubMed  CAS  Google Scholar 

  • Yu JK, Dake TM, Singh S, Benscher D, Li W, Gill B et al (2004) Development and mapping of EST-derived simple sequence repeat markers for hexaploid wheat. Genome 47:805–818. doi:10.1139/g04-057

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgments

Major financial support for this project was provided by Australian Grains R&D Corporation (GRDC), Regione Emilia Romagna (Italy), progetto PRITT, Misura 3.4-A CEREALAB and the European Union BIOEXPLOIT Integrated Project, contract no. 513959. We would like to acknowledge technical help from a number of colleagues from Diversity Arrays Technology Pty Ltd/Triticarte Pty Ltd (Grzegorz Uszynski, Jason Carling, Vanessa Caig, Ling Xia, Damian Jaccoud, Kasia Heller-Uszynska, Gosia Aschenbrenner-Kilian) and from DiSTA, University of Bologna (Sandra Stefanelli).

Author information

Authors and Affiliations

  1. Department of Agroenvironmental Sciences and Technology, University of Bologna, Viale Fanin 44, 40127, Bologna, Italy

    Paola Mantovani, Marco Maccaferri, Maria Corinna Sanguineti, Roberto Tuberosa & Ilaria Catizone

  2. Diversity Arrays Technology P/L and Triticarte Pty Ltd, 1 Wilf Crane Cr., Yarralumla, Canberra, ACT, 2600, Australia

    Ilaria Catizone, Peter Wenzl, Brent Thomson, Jason Carling, Eric Huttner & Andrzej Kilian

  3. Società Produttori Sementi Bologna, Research Division, Via Macero 1, 40050, Argelato, BO, Italy

    Enzo DeAmbrogio

Authors
  1. Paola Mantovani
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Marco Maccaferri
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Maria Corinna Sanguineti
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Roberto Tuberosa
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Ilaria Catizone
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Peter Wenzl
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Brent Thomson
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Jason Carling
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Eric Huttner
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Enzo DeAmbrogio
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. Andrzej Kilian
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Andrzej Kilian.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Mantovani, P., Maccaferri, M., Sanguineti, M.C. et al. An integrated DArT-SSR linkage map of durum wheat. Mol Breeding 22, 629–648 (2008). https://doi.org/10.1007/s11032-008-9205-3

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11032-008-9205-3

Keywords

Search

Navigation