Skip to main content
SpringerLink
Log in

Genetic diversity and linkage disequilibrium studies on a 3.1-Mb genomic region of chromosome 3B in European and Asian bread wheat (Triticum aestivum L.) populations

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

Abstract

Genetic diversity and linkage disequilibrium (LD) were investigated in 376 Asian and European accessions of bread wheat (Triticum aestivum L.). After a first and rapid screening about diversity and genetic structure at the whole genome scale using 70 simple sequence repeats (SSRs), we focused on a sequenced contig (ctg954) of 3.1 Mb located on the short arm of chromosome 3B of cv. Chinese Spring, using 32 SSRs and 10 single nucleotide polymorphisms. This contig is part of a multiple fungal resistance region. Mean polymorphism information content value on the 32 SSRs was slightly higher in the Asian genepool (0.396) than that for the European (0.329) pool. Compared with results at the whole genome scale, data from this 3.1-Mb region indicated similar trends in genetic diversity indices between both genepools. Population structure and molecular variance analyses demonstrated significant genetic differentiation and geographical subdivision in both groups of accessions. Concerning LD at the contig level, the European population had a significantly higher mean r 2 value (0.23) than the Asian population (0.18), indicating a stronger LD in the European material. With a mean of 1 marker every 74 kb, the resolution reached here allowed to perform a detailed comparative analysis of the LD and genetic diversity along the complete 3.1-Mb region in both genepools. A sliding-window approach revealed some interesting regions of the contig where LD is increasing when genetic diversity is decreasing. This study provides an in-depth understanding of molecular population genetics in European and Asian wheat gene pools, and prospects for association mapping of important sources of fungal disease resistance.

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

Similar content being viewed by others

References

  • Able JA, Langridge P, Milligan AS (2007) Capturing diversity in the cereals: many options but little promiscuity. Trends Plant Sci 12:71–79

    Article  CAS  PubMed  Google Scholar 

  • Balfourier F, Ravel C, Bochard AM, Exbrayat Vinson F, Boutet G, Sourdille P, Dufour F, Charmet G (2006) Développement utilisation et comparaison de différents types de marqueurs pour étudier la diversité parmi une collection de blé tendre. Les Actes du BRG 6:129–144

    Google Scholar 

  • Balfourier F, Roussel V, Strelchenko P, Exbrayat-Vinson F, Sourdille P, Boutet G, Koenig J, Ravel C, Mitrofanova O, Beckert M, Charmet G (2007) A worldwide bread wheat core collection arrayed in a 384-well plate. Theor Appl Genet 114:1265–1275

    Article  PubMed  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

    Article  PubMed  Google Scholar 

  • Brunner S, Keller B, Feuillet C (2003) A large rearrangement involving genes and low-copy DNA interrupts the microcollinearity between rice and barley at the Pph7 locus. Genetics 164:673–683

    CAS  PubMed  Google Scholar 

  • Chao S, Zhang WJ, Dubcovsky J, Sorrells M (2007) Evaluation of genetic diversity and genome-wide linkage disequilibrium among U.S. wheat (Triticum aestivum L.) germplasm representing different market classes. Crop Sci 47:1018–1030

    Article  CAS  Google Scholar 

  • Choulet F, Wicker T, Rustenholz C, Paux E, Salse J, Leroy P, Schlub S, Le Paslier MC, Magdelenat G, Gonthier C, Couloux A, Budak H, Breen J, Pumphrey M, Liu S, Kong X, Jia J, Gut M, Brunel D, Anderson JA, Gill BS, Appels R, Keller B, Feuillet C (2010) Megabase level sequencing reveals contrasted organization and evolution patterns of the wheat gene and transposable element spaces. Plant Cell (in press)

  • Dreher K, Khairallah M, Ribaut J-M, Morris M (2003) Money matters (I): costs of field and laboratory procedures associated with conventional and marker-assisted maize breeding at CIMMYT. Mol Breed 11:221–234

    Article  Google Scholar 

  • Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14:2611–2620

    Article  CAS  PubMed  Google Scholar 

  • Excoffier L, Laval G, Schneider S (2005) Arlequin ver. 3.0: an integrated software package for population genetics data analysis. Evol Bioinform Online 1:47–50

    CAS  PubMed  Google Scholar 

  • Feldman M (2000) Origin of cultivated wheat. In: Bonjean AP, Angus JW (eds) The world wheat book, a history of wheat breeding. TEC and DOC, London, pp 3–56

    Google Scholar 

  • Flint-Garcia SA, Thornsberry JM, Buckler ES (2003) Structure of linkage disequilibrium in plants. Annu Rev Plant Biol 54:357–374

    Article  CAS  PubMed  Google Scholar 

  • Frankham R (2005) Genetics and extinction. Biol Conserv 126:131–140

    Article  Google Scholar 

  • Gaut BS, Long AD (2003) The lowdown on linkage disequilibrium. Plant Cell 15:1502–1506

    Article  CAS  PubMed  Google Scholar 

  • Ghimire SK, Akashi Y, Maitani C, Nakanishi M, Kato K (2005) Genetic diversity and geographical differentiation in Asian common wheat (Triticum aestivum L.), revealed by the analysis of peroxidase and esterase isozymes. Breed Sci 55:175–185

    Article  CAS  Google Scholar 

  • Hao CY, Wang LF, Zhang XY, You GX, Dong YS, Jia JZ, Liu X, Shang XW, Liu SC, Cao YS (2006) Genetic diversity in Chinese modern wheat varieties revealed by microsatellite markers. Sci China C Life Sci 49:218–226

    Article  CAS  PubMed  Google Scholar 

  • Hao CY, Dong YS, Wang LF, You GX, Zhang HN, Ge HM, Jia JZ, Zhang XY (2008) Genetic diversity and construction of core collection in Chinese wheat genetic resources. Chin Sci Bull 53:1518–1526

    Article  CAS  Google Scholar 

  • He ZH, Rajaram S, Xin ZY, Huang GZ (2001) A history of wheat breeding in China. CIMMYT, Mexico, D.F.

    Google Scholar 

  • Horvath A, Didier A, Koenig J, Exbrayat F, Charmet G, Balfourier F (2009) Analysis of diversity and linkage disequilibrium along chromosome 3B of bread wheat (Triticum aestivum L.). Theor Appl Genet. doi:10.1007/s00122-1158-8

  • Huang XQ, Borner A, Röder MS, Ganal MW (2002) Assessing genetic diversity of wheat (Triticum aestivum L.) germplasm using microsatellite markers. Theor Appl Genet 105:699–707

    Article  CAS  PubMed  Google Scholar 

  • Kilian B, Özkan H, Pozzi C, Salamini F (2009) Domestication of the Triticeae in the Fertile Crescent. In: Feuillet C, Muehlbauer G (eds) Genetics and genomics of the Triticeae plant genetics and genomics: crops and models 7. Springer, Berlin, pp 81–119

    Google Scholar 

  • Liu K, Muse SV (2005) PowerMarker: integrated analysis environment for genetic marker data. Bioinformatics 21:2128–2129

    Article  CAS  PubMed  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 15:271–289

    Article  CAS  Google Scholar 

  • Mitrofanova OP, Strelchenko PP, Konarev AV, Balfourier F (2009) Genetic differentiation of hexaploid wheat inferred from analysis of microsatellite loci. Russ J Genet 45(11):1351–1359

    Article  CAS  Google Scholar 

  • Morris M, Dreher K, Ribaut JM, Khairallah M (2003) Money matters (I): costs of maize inbred line conversion schemes at CIMMYT using conventional and marker-assisted selection. Mol Breed 11:235–247

    Article  Google Scholar 

  • Nei M (1973) Analysis of gene diversity in subdivided populations. PNAS 70:3321–3323

    Article  CAS  PubMed  Google Scholar 

  • Nesbitt M (2001) Wheat evolution: integrating archaeological and biological evidence. The Linnean (special issue) 3:37–59

    Google Scholar 

  • Nicot N, Chiquet V, Gandon B, Amilhat L, Legeai F, Leroy F, 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 

  • Nordborg M, Tavare S (2002) Linkage disequilibrium: what history has to tell us. Trends Genet 18:83–90

    Article  CAS  PubMed  Google Scholar 

  • Palaisa K, Morgante M, Williams M, Rafalski A (2003) Contrasting effects of selection on sequence diversity and linkage disequilibrium at two phytoene synthase loci. Plant Cell 15:1795–1806

    Article  CAS  PubMed  Google Scholar 

  • Paux E, Roger D, Badaeva E, Gay G, Bernard M, Sourdille P, Feuillet C (2006) Characterizing the composition and evolution of homoeologous genomes in hexaploid wheat through BAC-end sequencing on chromosome 3B. Plant J 48:463–474

    Article  CAS  PubMed  Google Scholar 

  • Paux E, Sourdille P, Salse J, Saintenac C, Choulet F, Leroy P et al (2008) A physical map of the 1-gigabase bread wheat chromosome 3B. Science 322:101–104

    Article  CAS  PubMed  Google Scholar 

  • Paux E, Faure S, Choulet F, Roger D, Gauthier V, Martinant JP, Sourdille P, Balfourier F, Le Paslier MC, Chauveau A, Cakir M, Gandon B, Feuillet C (2010) Insertion site-based polymorphism markers open new perspectives for genome saturation and marker-assisted selection in wheat. Plant Biotechnol J 8:196–210

    Article  CAS  PubMed  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 

  • Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure from multilocus genotype data. Genetics 155:945–959

    CAS  PubMed  Google Scholar 

  • Rafalski A (2002) Application of single nucleotide polymorphisms in crop genetics. Curr Opin Plant Biol 5:94–100

    Article  CAS  PubMed  Google Scholar 

  • Rafalski A, Morgante M (2004) Corn and humans: recombination and linkage disequilibrium in two genomes of similar size. Trends Genet 20:103–111

    Article  CAS  PubMed  Google Scholar 

  • Raquin AL, Brabant P, Rhone B, Balfourier F, Leroy P, Goldringer I (2008) Soft selective sweep near a gene that increases plant height in wheat. Mol Ecol 17:741–756

    Article  PubMed  Google Scholar 

  • Ravel C, Choulet F, Dardevet M, Exbrayat-Vinson F, Sourdille P, Balfourier F (2009) Linkage disequilibrium at different scales on 3B chromosome of bread wheat. In: Proceedings of ITMI international conference, 31 August–4 September, Clermont-Ferrand, France, p 132

  • Reich DE, Cargill M, Bolk S, Ireland J, Sabeti PC, Richter DJ, Lavery T, Kouyoumjian R, Farhadian SF, Ward R, Lander ES (2001) Linkage disequilibrium in the human genome. Nature 411:199–204

    Article  CAS  PubMed  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 

  • Röder MS, Wendehake K, Korzun V, Bredemeijer G, Laborie D, Bertrand L, Isaac P, Rendell S, Jackson J, Cooke RJ, Vosman B, Ganal MW (2002) Construction and analysis of a microsatellite-based database of European wheat varieties. Theor Appl Genet 106:67–73

    PubMed  Google Scholar 

  • Roussel V, Leisova L, Exbrayat F, Stehno Z, Balfourier F (2005) SSR allelic diversity changes in 480 European bread wheat varieties released from 1840 to 2000. Theor Appl Genet 111:162–170

    Article  CAS  PubMed  Google Scholar 

  • Saintenac C, Falque M, Martin O, Paux E, Feuillet C, Sourdille P (2009) Detailed recombination studies along chromosome 3B provide new insight into crossover distribution in wheat. Genetics 181:393–403

    Article  CAS  PubMed  Google Scholar 

  • Schlumbaum A, Neuhaus JM, Jacomet S (1998) Coexistence of tetraploid and hexaploid naked wheat in a neolithic lake dwelling of central Europe. Evidence from morphology and ancient DNA. J Archaeol Sci 25:1111–1118

    Article  Google Scholar 

  • Somers DJ, Banks T, DePauw R, Fox S, Clarke J, Pozniak C, McCartney C (2007) Genome-wide linkage disequilibrium analysis in bread wheat and durum wheat. Genome 50:557–567

    Article  CAS  PubMed  Google Scholar 

  • Tanksley SD, Young ND, Paterson AH, Bonierbale MW (1989) RELF mapping in plant breeding: new tools for an old science. Biotechniques 7:257–264

    Article  CAS  Google Scholar 

  • Väli Ü, Einarsson A, Waits L, Ellegren H (2008) To what extent do microsatellite markers reflect genome-wide genetic diversity in natural populations. Mol Ecol 17:3808–3817

    Article  PubMed  Google Scholar 

  • Wang LF, Balfourier F, Hao CY, Exbrayat-Vinson F, Dong YC, Ge HM, Zhang XY (2007) Comparison of genetic diversity level between European and East-Asian wheat collections using SSR markers. Sci Agric Sin 40:2667–2678

    CAS  Google Scholar 

  • Wilson LM, Whitt SR, Ibanez AM, Rocheford TR, Goodman MM, Buckler ES (2004) Dissection of maize kernel composition and starch production by candidate gene association. Plant Cell 16:2719–2733

    Article  CAS  PubMed  Google Scholar 

  • Yu JM, Buckler ES (2006) Genetic association mapping and genome organization of maize. Curr Opin Biotechnol 17:155–160

    CAS  PubMed  Google Scholar 

  • Zhang LY, Bernard M, Leroy P, Feuillet C, Sourdille P (2005) High transferability of bread wheat EST-derived SSRs to other cereals. Theor Appl Genet 111:677–687

    Article  CAS  PubMed  Google Scholar 

  • Zhang ZW, Bradbury PJ, Kroon DE, Casstevens TM, Buckler ES (2006) TASSEL 2.0: a software package for association and diversity analyses in plants and animals (http://www.maizegenetics.net). In: Plant and animal genomes XIV conference, Poster P956/CP012, San Diego, USA

  • Zwart RS, Muylle H, Bockstaele EV, Roldán-Ruiz I (2008) Evaluation of genetic diversity of Fusarium head blight resistance in European winter wheat. Theor Appl Genet 117:813–828

    Article  PubMed  Google Scholar 

Download references

Acknowledgments

This work was supported by a Project of Advanced Research (PRA 005) between the French National Institute for Agronomical Research (INRA) and the Chinese Academy of Agriculture Science. It was also funded by the EXEGESE-BLE and Genoplante-SMART projects from the French National Research Agency. The authors are grateful to the MRI from INRA for providing a grant and funding for the experiment. They also gratefully appreciate Prof. Robert A McIntosh of the University of Sydney for his help on English editing.

Author information

Authors and Affiliations

  1. INRA UMR 1095, Genetics Diversity and Ecophysiology of Cereals, 234 Avenue du Brezet, 63100, Clermont-Ferrand, France

    C. Y. Hao, M. R. Perretant, F. Choulet, L. F. Wang, E. Paux, P. Sourdille, C. Feuillet & Francois Balfourier

  2. Key Laboratory of Crop Germplasm Resources and Utilization, Ministry of Agriculture, CAAS, Beijing, 100081, China

    C. Y. Hao, L. F. Wang & X. Y. Zhang

  3. The National Key Facility for Crop Gene Resources and Genetic Improvement, CAAS, Beijing, 100081, China

    C. Y. Hao, L. F. Wang & X. Y. Zhang

  4. Institute of Crop Science, CAAS, Beijing, 100081, China

    C. Y. Hao, L. F. Wang & X. Y. Zhang

Authors
  1. C. Y. Hao
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. M. R. Perretant
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. F. Choulet
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. L. F. Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. E. Paux
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. P. Sourdille
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. X. Y. Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. C. Feuillet
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Francois Balfourier
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Francois Balfourier.

Additional information

Communicated by A. Graner.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (DOC 1154 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Hao, C.Y., Perretant, M.R., Choulet, F. et al. Genetic diversity and linkage disequilibrium studies on a 3.1-Mb genomic region of chromosome 3B in European and Asian bread wheat (Triticum aestivum L.) populations. Theor Appl Genet 121, 1209–1225 (2010). https://doi.org/10.1007/s00122-010-1382-x

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00122-010-1382-x

Keywords

Search

Navigation