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

Theoretical and Applied Genetics

Volumn 121, Issue 7, 2010, Pages 1209-1225

  Hao, C Y ^a,b   Perretant, M R ^a   Choulet, F ^a   Wang, L F ^a,b   Paux, E ^a   Sourdille, P ^a   Zhang, X Y ^b   Feuillet, C ^a   Balfourier, Francois ^a  

^a Diversity and Ecophysiology of Cereals   (France)

^b INSTITUTE OF PLANT PROTECTION   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ASSOCIATION MAPPING; BREAD WHEAT; CHINESE SPRINGS; COMPARATIVE ANALYSIS; FUNGAL DISEASE RESISTANCE; GENETIC DIFFERENTIATION; GENETIC DIVERSITY; GENETIC STRUCTURE; GENOMIC REGIONS; IN-DEPTH UNDERSTANDING; INFORMATION CONTENTS; LINKAGE DISEQUILIBRIUM; MOLECULAR POPULATION; MOLECULAR VARIANCE ANALYSIS; POPULATION STRUCTURES; RAPID SCREENING; SIMPLE SEQUENCE REPEATS; SINGLE NUCLEOTIDE POLYMORPHISMS; SLIDING-WINDOW; WHEAT GENES;

FOOD PRODUCTS; GENES; LAKES; PLANTS (BOTANY); POLYMORPHISM;

BIODIVERSITY;

MICROSATELLITE DNA;

ARTICLE; ASIA; CONTIG MAPPING; EUROPE; GENE LINKAGE DISEQUILIBRIUM; GENE POOL; GENETIC MARKER; GENETICS; PLANT CHROMOSOME; PLANT GENOME; PLANT IMMUNITY; SINGLE NUCLEOTIDE POLYMORPHISM; WHEAT;

ASIA; CHROMOSOMES, PLANT; CONTIG MAPPING; EUROPE; GENE POOL; GENETIC MARKERS; GENOME, PLANT; LINKAGE DISEQUILIBRIUM; MICROSATELLITE REPEATS; PLANT IMMUNITY; POLYMORPHISM, SINGLE NUCLEOTIDE; TRITICUM;

TRITICUM AESTIVUM;

EID: 78049275764     PISSN: 00405752     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00122-010-1382-x     Document Type: Article

References (54)

1. Able JA, Langridge P, Milligan AS (2007) Capturing diversity in the cereals: many options but little promiscuity. Trends Plant Sci 12: 71-79.
2. 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.
3. 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.
4. Breseghello F, Sorrells ME (2006) Association mapping of kernel size and milling quality in wheat (Triticum aestivum L.) cultivars. Genetics 172: 1165-1177.
5. 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.
6. 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.
7. 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).
8. 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.
9. 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.
10. 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.
11. 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.
12. Flint-Garcia SA, Thornsberry JM, Buckler ES (2003) Structure of linkage disequilibrium in plants. Annu Rev Plant Biol 54: 357-374.
13. Frankham R (2005) Genetics and extinction. Biol Conserv 126: 131-140.
14. Gaut BS, Long AD (2003) The lowdown on linkage disequilibrium. Plant Cell 15: 1502-1506.
15. 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.
16. 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.
17. 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.
18. He ZH, Rajaram S, Xin ZY, Huang GZ (2001) A history of wheat breeding in China. CIMMYT, Mexico, D. F.
19. 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.
20. 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.
21. 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.
22. Liu K, Muse SV (2005) PowerMarker: integrated analysis environment for genetic marker data. Bioinformatics 21: 2128-2129.
23. 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.
24. 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.
25. 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.
26. Nei M (1973) Analysis of gene diversity in subdivided populations. PNAS 70: 3321-3323.
27. Nesbitt M (2001) Wheat evolution: integrating archaeological and biological evidence. The Linnean (special issue) 3: 37-59.
28. 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.
29. Nordborg M, Tavare S (2002) Linkage disequilibrium: what history has to tell us. Trends Genet 18: 83-90.
30. 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.
31. 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.
32. 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.
33. 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.
34. 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.
35. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure from multilocus genotype data. Genetics 155: 945-959.
36. Rafalski A (2002) Application of single nucleotide polymorphisms in crop genetics. Curr Opin Plant Biol 5: 94-100.
37. Rafalski A, Morgante M (2004) Corn and humans: recombination and linkage disequilibrium in two genomes of similar size. Trends Genet 20: 103-111.
38. 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.
39. 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.
40. 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.
41. Röder MS, Korzun V, Wendehake K, Plaschke J, Tixier MH, Leroy P, Ganal MW (1998) A microsatellite map of wheat. Genetics 149: 2007-2023.
42. 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.
43. 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.
44. 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.
45. 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.
46. 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.
47. Tanksley SD, Young ND, Paterson AH, Bonierbale MW (1989) RELF mapping in plant breeding: new tools for an old science. Biotechniques 7: 257-264.
48. 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.
49. 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.
50. 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.
51. Yu JM, Buckler ES (2006) Genetic association mapping and genome organization of maize. Curr Opin Biotechnol 17: 155-160.
52. 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.
53. 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.
54. 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.