Advertisement

Theoretical and Applied Genetics

, 119:1523 | Cite as

Analysis of diversity and linkage disequilibrium along chromosome 3B of bread wheat (Triticum aestivum L.)

  • Aniko Horvath
  • Audrey Didier
  • Jean Koenig
  • Florence Exbrayat
  • Gilles Charmet
  • François BalfourierEmail author
Original Paper

Abstract

A highly polymorphic core collection of bread wheat and a more narrow-based breeding material, gathered from pedigrees of seven modern cultivars, was analysed in order to compare genetic diversity indices and linkage disequilibrium (LD) patterns along the chromosome 3B with microsatellite (SSR) and Diversity Arrays Technology markers. Five ancestral gene pools could be identified within the core collection, indicating a strong geographical structure (Northwest Europe, Southeast Europe, CIMMYT–ICARDA group, Asia, Nepal). The breeding material showed a temporal structure, corresponding to different periods of breeding programmes [old varieties (from old landraces to 1919), semi-modern varieties (1920–1959), modern varieties (1960–2006)]. Basic statistics showed a higher genetic diversity in the core collection than in the breeding material, indicating a stronger selection pressure in this latter material. More generally, the chromosome 3B had a lower diversity than the whole B-genome. LD was weak in all studied materials. Amongst geographical groups, the CIMMYT–ICARDA pool presented the longest ranged LD in contrast to Asian accessions. In the breeding material, LD increased from old cultivars to modern varieties. Genitors of seven modern cultivars were found to be different; most marker pairs in significant LD were observed amongst genitors of Alexandre and Koreli varieties, indicating an important inbreeding effect. At low genetic distances (0–5 cM), the breeding material had higher LD than the core collection, but globally the two materials had similar values in all classes. Marker pairs in significant LD are generally observed around the centromere in both arms and at distal position on the short arm of the chromosome 3B.

Keywords

Linkage Disequilibrium Simple Sequence Repeat Marker Bread Wheat Fusarium Head Blight Core Collection 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Notes

Acknowledgments

The authors are grateful to P. Sourdille for providing CFA, CFB, CFE microsatellite primer pairs and thank Genoplante Consortium, RAGT and Syngenta firms for GPW, WMM and NW microsatellite primers, respectively. This work is part of the SDD project (Semences De Demain) which has been financed by the “Industry competitiveness Fund” of the French Ministry of Industry (http://www.competitivite.gouv.fr) and labelled by the pole “Céréales vallée” (http://cereales-vallee.org/). It is also a part of the EXEGESE project founded by NRA (French National Research Agency).

Supplementary material

122_2009_1153_MOESM1_ESM.pdf (775 kb)
Supplementary material (PDF 774 kb)

References

  1. Able JA, Langridge P, Milligan AS (2007) Capturing diversity in the cereals: many options but little promiscuity. Trends Plant Sci 12(2):71–79CrossRefPubMedGoogle Scholar
  2. Balfourier F, Roussel V, Strelchenko P, Exbrayat-Winson 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 114:1265–1275CrossRefPubMedGoogle Scholar
  3. Baron M, Bastergue P, Branlard G, Cauderon Y, Guiard J, Jahier J, Lonnet P, Quandalle C, Ronsin T, Rousset M, Triverio F, Trottet M (2006) Le blé tendre. In: Doré C, Varoquaux F (eds) Histoire et amélioration de cinquante plantes cultivées. INRA Editions, Paris, France, pp 137–161Google Scholar
  4. Belkhir K, Borsa P, Chikhi L, Raufaste N, Bonhomme F (2004) Genetix 4.05.2, Logiciel sous Windows™ pour la Génétique des Populations. Laboratoire Génome, Populations, Interactions, CNRS UMR 5000, Université de Montpellier II, Montpellier, FranceGoogle Scholar
  5. Bonjean AP, Doussinault G, Stragliati J (2001) French wheat pool. In: Bonjean AP, Angus WP (eds) The world wheat book. A history of wheat breeding. Intercept Ltd., Editions Tec & Doc, Lavoisier Publishing Inc., Londres, Paris, New York, pp 127–165Google Scholar
  6. Bonnier G, Douin R (1990) La grande flore en couleurs de Gaston Bonnier, France, Suisse, Belgique et pays voisins. Belin Editions, Paris, France, pp 1–1401Google Scholar
  7. Bordes J, Branlard G, Oury F-X, Charmet G, Balfourier F (2008) Agronomic characteristics, grain quality and flour rheology of 372 bread wheats in a worldwide core collection. J Cereal Sci. doi: 10.1016/j.jcs.2008.05.005
  8. Breseghello F, Sorrels ME (2006) Association mapping of kernel size and milling quality in wheat (Triticum aestivum L.) cultivars. Genetics 172:1165–1177CrossRefPubMedGoogle Scholar
  9. Chao S, Zhang W, Dubcovsky J, Sorrels ME (2007) Evaluation of genetic diversity and genome-wide linkage disequilibrium among US wheat (Triticum aestivum L.) germplasm representing different mark classes. Crop Sci 47:1018–1030CrossRefGoogle Scholar
  10. Eivazi AR, Naghavi MR, Hajheidari M, Pirseyedi SM, Ghaffari MR, Mohammadi SA, Majidi I, Salekdeh GH, Mardi M (2008) Assessing wheat (Triticum aestivum L.) genetic diversity using quality traits, amplified fragment length polymorphisms, simple sequence repeats and proteome analysis. Ann Appl Biol 152:81–91CrossRefGoogle Scholar
  11. Endo TR, Gill BS (1996) The deletion stocks of common wheat. J Hered 87:295–307Google Scholar
  12. Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14:2611–2620CrossRefPubMedGoogle Scholar
  13. FAOSTAT (2008) http://faostat.fao.org/ (last accessed July 2008)
  14. Farnir F, Coppieters W, Arranz J-J, Berzi P, Cambisano N, Grisart B, Karim L, Marcq F, Moreau L, Mni M, Nezer C, Simon P, Vanmanshoven P, Wagenaar D, Georges M (2000) Extensive genome-wide linkage disequilibrium in cattle. Genome Res 10:220–227CrossRefPubMedGoogle Scholar
  15. Felsenstein J (2004) PHYLIP (Phylogeny Inference Package) version 3.6. Department of Genome Sciences, University of Washington, Seattle, USAGoogle Scholar
  16. Flint-Garcia SA, Thornsberry JM, Buckler ES IV (2003) Structure of linkage disequilibrium in plants. Annu Rev Plant Biol 54:357–374CrossRefPubMedGoogle Scholar
  17. Gervais L, Derdryver F, Morlais J-Y, Bodusseau V, Negre S, Bilous M, Groos C, Trottet M (2003) Mapping of quantitative trait loci for field resistance to Fusarium head blight in an European winter wheat. Theor Appl Genet 106:961–970PubMedGoogle Scholar
  18. Gill BS, Appels R, Botha-Oberholster A-M, Buell CR, Bennetzen JL, Chalhoub B, Chumley F, Dvorak J, Iwanaga M, Keller B, Li W, McCombie WR, Ogihara Y, Quetier F, Sasaki T (2004) A workshop report on wheat genome sequencing: international genome research on wheat consortium. Genetics 168:1087–1096CrossRefPubMedGoogle Scholar
  19. Groos C, Gay G, Perretant M-R, Gervais L, Bernard M, Derdryver F, Charmet G (2002) Study of the relationship between pre-harvest sprouting and grain color by quantitative trait loci analysis in a white × red grain bread-wheat cross. Theor Appl Genet 104:39–47CrossRefPubMedGoogle Scholar
  20. Gupta PK, Balyan HS, Edwards KJ, Isaac P, Korzun V, Roder MS, Gautier M-F, 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 105:413–422CrossRefPubMedGoogle Scholar
  21. Hao C, Lanfen W, Xueyong Z, Guangxia Y, Yushen D, Jizeng J, Xu L, Xunwu S, Sancai L, Yongsheng C (2006) Genetic diversity in Chinese modern wheat varieties revealed by microsatellite markers. Sci China C Life Sci 49:218–226CrossRefPubMedGoogle Scholar
  22. Haseneyer G, Ravel C, Dardevet M, Balfourier F, Sourdille P, Charmet G, Brunel D, Sauer S, Geiger HH, Graner A, Stracke S (2008) High level of conservation between genes coding for the GAMYB transcription factor in barley (Hordeum vulgare L.) and bread wheat (Triticum aestivum L.) collections. Theor Appl Genet 117:321–331CrossRefPubMedGoogle Scholar
  23. Khush GS (2001) Green revolution: the way forward. Nat Rev Genet 2:815–822CrossRefPubMedGoogle Scholar
  24. Landjeva S, Korzun V, Ganeva G (2006) Evaluation of genetic diversity among Bulgarian winter wheat (Triticum aestivum L.) varieties during the period 1925–2003 using microsatellites. Genet Res Crop Evol 53:1605–1614CrossRefGoogle Scholar
  25. Laperche A, Brancourt-Hulmel M, Heumez E, Gardet O, Hanocq E, Devienne-Barret F, Le Gouis J (2007) Using genotype × nitrogen interaction variables to evaluate the QTL involved in wheat tolerance to nitrogen constraints. Theor Appl Genet 115:399–415CrossRefPubMedGoogle Scholar
  26. Lee J-H, Ma Y, Wako T, Li LC, Kim K-Y, Park S-W, Uchiyama S, Fukui K (2004) Flow karyotypes and chromosomal DNA contents of genus Triticum species and rye (Secale cereale). Chromosome Res 12:93–102CrossRefPubMedGoogle Scholar
  27. Liu F, Sun G-L, Salomon B, Von Bothmer R (2002) Characterization of genetic diversity in core collection accessions of wild barley, Hordeum vulgare ssp. spontaneum. Hereditas 136:67–73CrossRefPubMedGoogle Scholar
  28. Ma HX, Zhang KM, Gao L, Bai GH, Chen HG, Cai ZX, Lu WZ (2006) Quantitative trait loci for resistance to fusarium head blight and deoxynivalenol accumulation in Wangshuibai wheat under field conditions. Plant Pathol 55:739–745CrossRefGoogle Scholar
  29. Maccaferri M, Sanguineti MC, Noli E, Tuberosa R (2005) Population structure and long-range linkage disequilibrium in a durum wheat elite collection. Mol Breed 15:271–289CrossRefGoogle Scholar
  30. Malysheva-Otto LV, Roder MS (2006) Haplotype diversity in the endosperm specific β-amylase gene Bmy1 of cultivated barley (Hordeum vulgare L.). Mol Breed 18:143–156CrossRefGoogle Scholar
  31. Malysheva-Otto LV, Ganal MW, Roder MS (2006) Analysis of molecular diversity, population structure and linkage disequilibrium in a worldwide survey of cultivated barley germplasm (Hordeum vulgare L.). BMC Genet 7(6). doi: 10.1186/1471-2156-7-6
  32. McNeil MD, Kota R, Paux E, Dunn D, McLean R, Feuillet C, Li D, Kong X, Lagudah E, Zhang JC, Jia JZ, Spielmeyer W, Bellgard M, Appels R (2008) BAC-derived markers for assaying the stem rust resistance gene, Sr2, in wheat breeding programmes. Mol Breed 22:15–24CrossRefGoogle Scholar
  33. Nei M (1973) Analysis of gene diversity in subdivised populations. PNAS 70:3321–3323CrossRefPubMedGoogle Scholar
  34. Nei M (1978) Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89:583–590PubMedGoogle Scholar
  35. Ozkan H, Brandolini A, Schafer-Pregl R, Salamini F (2002) AFLP analysis of a collection of tetraploid wheats indicates the origin of emmer and hard wheat domestication in southeast Turkey. Mol Biol Evol 19(10):1797–1801PubMedGoogle Scholar
  36. Page RDM (1996) TREEVIEW: an application to display phylogenetic trees on personal computers. Comput Appl Biosci 12:357–358PubMedGoogle Scholar
  37. 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 48:463–474CrossRefPubMedGoogle Scholar
  38. Paux E, Legeai F, Guilhot N, Adam-Blondon A-F, Alaux M, Salse J, Sourdille P, Leroy P, Feuillet C (2008a) Physical mapping in large genomes: accelerating anchoring of BAC contigs to genetic maps through in silico analysis. Funct Integr Genom 8:29–32CrossRefGoogle Scholar
  39. Paux E, Sourdille P, Salse J, Saintenac C, Choulet F, Leroy P, Korol A, Michalak M, Kianian SF, Spielmeyer W, Lagudah E, Somers D, Kilian A, Alaux M, Vautrin S, Berges H, Eversole K, Appels R, Safar J, Simkova H, Dolezel J, Bernard M, Feuillet C (2008b) A physical map of the 1-gigabase bread wheat chromosome 3B. Science 322:101–104CrossRefPubMedGoogle Scholar
  40. Perrier X, Jacquemoud-Collet JP (2006) DARwin software. http://darwin.cirad.fr/darwin
  41. Petit RJ, El Mousadik A, Pons O (1998) Identifying populations for conservation on the basis of genetic markers. Conserv Biol 12(4):844–855CrossRefGoogle Scholar
  42. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959PubMedGoogle Scholar
  43. Qi LL, Echalier B, Chao S, Lazo GR, Butler GE, Anderson OD, Akhunov ED, Dvorak J, Linkiewicz AM, Ratnasiri A, Dubcovsky J, Bermudez-Kandianis CE, Greene RA, Kantety R, La Rota CM, Munkvold JD, Sorrels SF, Sorrels ME, Dilbirligi M, Sidhu D, Erayman M, Randhawa HS, Sandhu D, Bondareva SN, Gill KS, Mahmoud AA, Ma X-F, Miftahudin, 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 168:701–712CrossRefPubMedGoogle Scholar
  44. R Development Core Team (2006) R: a language and environment for statistical computing, version 2.4.0. R Foundation for Statistical Computing, Vienna, AustriaGoogle Scholar
  45. Rafalski A, Morgante M (2004) Corn and humans: recombination and linkage disequilibrium in two genomes of similar size. Trends Genet 20(2):103–111CrossRefPubMedGoogle Scholar
  46. Remington DL, Thornsberry JM, Matsuoka Y, Wilson LM, Whitt SR, Doebley J, Kresovich S, Goodman MM, Buckler ES IV (2001) Structure of linkage disequilibrium and phenotypic associations in the maize genome. PNAS 98:11479–11484CrossRefPubMedGoogle Scholar
  47. Roder MS, Korzun V, Wendehake K, Plaschke J, Tixier M-H, Leroy P, Ganal MW (1998) A microsatellite map of wheat. Genetics 149:2007–2023PubMedGoogle Scholar
  48. Roder 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 106:67–73PubMedGoogle Scholar
  49. Roussel V, Koenig J, Beckert M, Balfourier F (2004) Molecular diversity in French bread wheat accessions related to temporal trends and breeding programmes. Theor Appl Genet 108:920–930CrossRefPubMedGoogle Scholar
  50. 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 111:162–170CrossRefPubMedGoogle Scholar
  51. Routray P, Basha O, Garg M, Singh NK, Dhaliwal HS (2007) Genetic diversity of landraces of wheat (Triticum aestivum L.) from hilly areas of Uttaranchal, India. Genet Res Crop Evol 54:1315–1326CrossRefGoogle Scholar
  52. Saintenac C, Choulet F, Faure S, Paux E, Feuillet C, Sourdille P (2008) Recombination analysis on bread wheat chromosome 3B. In: Proceedings of the 11th international wheat genetics symposium. Sydney University Press, Brisbane, AustraliaGoogle Scholar
  53. Salamini F, Ozkan H, Brandolini A, Schafer-Pregl R, Martin W (2002) Genetics and geography of wild cereal domestication in the Near East. Genetics 3:429–441PubMedGoogle Scholar
  54. Seguin M, Attard A, Bataillon T, Billot C, Cenci A, Chantret N, Courtois B, David J, Deu M, El Azhari N, Glaszmann J-C, Glemin S, Haudry A, Le Guen V, Maynadier M, Pomies V, Ronfort J, Tsitronne A, Weber C (2006) Analyse et prédiction des patrons de déséquilibre de liaison dans les collections de ressources génétiques de plantes pérennes ou annuelles, autogames ou allogames. Les Actes du BRG 6:57–74Google Scholar
  55. Shen X, Francki MG, Ohm HW (2006) A resistance-like gene identified by EST mapping and its association with a QTL controlling Fusarium head blight infection on wheat chromosome 3B. Genome 49:631–635CrossRefPubMedGoogle Scholar
  56. Singh PK, Gonzalez-Hernandez JL, Mergoum M, Ali S, Adhikari TB, Kianian SF, Elias EM, Hughes GR (2006) Identification and molecular mapping of a gene conferring resistance to Pyrenophora tritici-repentis race 3 in tetraploid wheat. Phytopathology 96:885–889CrossRefPubMedGoogle Scholar
  57. Somers DJ, Isaac P, Edwards K (2004) A high-density microsatellite consensus map for bread wheat (Triticum aestivum L.). Theor Appl Genet 109:1105–1114CrossRefPubMedGoogle Scholar
  58. 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 50:557–567CrossRefPubMedGoogle Scholar
  59. Sourdille P, Guyomarc’h H, Baron C, Gandon B, Chiquet V, Artiguenave F, Edwards K, Foisset N, Dufour P (2001) Improvement of the genetic maps of wheat using new microsatellite markers. In: Abstracts 167, plant and animal genome IX conference, San Diego, USAGoogle Scholar
  60. Tadesse W, Hsam SLK, Wenzel G, Zeller FJ (2008) Chromosome location of a gene conferring resistance to Pyrenophora tritici-repentis in Ethiopian wheat cultivars. Euphytica 162:423–430CrossRefGoogle Scholar
  61. Tanyolac B, Linton E, Ozkan H (2003) Low genetic diversity in wild emmer (T. turgidum L. subsp. dicoccoides (Korn. ex Asch. et Graebn.) Thell.) from South-eastern Turkey revealed by restriction fragment length polymorphism. Genet Res Crop Evol 50:829–833CrossRefGoogle Scholar
  62. van Berloo R, Hutten RC (2005) Peditree: pedigree database analysis and visualisation for breeding and science. J Hered 96(4):465–468CrossRefPubMedGoogle Scholar
  63. Vrana J, Kubalakova M, Simkova H, Cihalikova J, Lysak MA, Dolezel J (2000) Flow sorting of mitotic chromosomes in common wheat (Triticum aestivum L.). Genetics 156:2033–2041PubMedGoogle Scholar
  64. Wenzl P, Carling J, Kudrna D, Jaccoud D, Huttner E, Kleinhofs A, Kilian A (2004) Diversity Arrays Technology (DArT) for whole-genome profiling of barley. PNAS 101:9915–9920CrossRefPubMedGoogle Scholar
  65. White J, Law JR, MacKay I, Chalmers KJ, Smith JSC, Kilian A, Powell W (2008) The genetic diversity of UK, US and Australian cultivars of Triticum aestivum measured by DArT markers and considered by genome. Theor Appl Genet 116:439–453CrossRefPubMedGoogle Scholar
  66. Zhang G, Mergoum M (2007) Molecular mapping of kernel shattering and its association with Fusarium head blight resistance in a Sumai3 derived population. Theor Appl Genet 115:757–766CrossRefPubMedGoogle Scholar
  67. 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 111:677–687CrossRefPubMedGoogle Scholar
  68. Zhang Z, Bradbury PJ, Kroon DE, Casstevens TM, Buckler ES (2006) TASSEL 2.0: a software package for association and diversity analyses in plants and animals (www.maizegenetics.net). In: Plant and animal genomes XIV conference, poster P956/CP012, San Diego, USA

Copyright information

© Springer-Verlag 2009

Authors and Affiliations

  • Aniko Horvath
    • 1
    • 2
  • Audrey Didier
    • 1
  • Jean Koenig
    • 1
  • Florence Exbrayat
    • 1
  • Gilles Charmet
    • 1
  • François Balfourier
    • 1
    Email author
  1. 1.INRA, UMR1095 Genetics, Diversity and Ecophysiology of CerealsClermont-FerrandFrance
  2. 2.INRA, UR419 Fruit SpeciesVillenave d’OrnonFrance

Personalised recommendations