Microsatellite diversity and broad scale geographic structure in a model legume: Building a set of nested core collection for studying naturally occurring variation in Medicago truncatula

BMC Plant Biology

Volumn 6, Issue , 2006, Pages

  Ronfort, Joëlle ^a   Bataillon, Thomas ^a,b   Santoni, Sylvain ^a   Delalande, Magalie ^a   David, Jacques L ^a   Prosperi, Jean Marie ^a  

^a CEMAGREF   (France)

^b AARHUS UNIVERSITY   (Denmark)

Author keywords

[No Author keywords available]

Indexed keywords

MEDICAGO TRUNCATULA;

MICROSATELLITE DNA; PLANT DNA;

BARREL MEDIC; GENETIC VARIABILITY; GENETICS; GENOTYPE; PLANT GENE;

DNA, PLANT; GENES, PLANT; GENETIC VARIATION; GENOTYPE; MEDICAGO TRUNCATULA; MICROSATELLITE REPEATS;

EID: 33846564955     PISSN: None     EISSN: 14712229     Source Type: Journal    
DOI: 10.1186/1471-2229-6-28     Document Type: Article

References (42)

1. Initiative. TAG: Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 2000, 408(6814):796-815.
2. Goff SA, Ricke D, Lan TH, Presting G, Wang R, Dunn M, Glazebrook J, Sessions A, Oeller P, Varma H, Hadley D, Hutchison D, Martin C, Katagiri F, Lange BM, Moughamer T, Xia Y, Budworth P, Zhong J, Miguel T, Paszkowski U, Zhang S, Colbert M, Sun WL, Chen L, Cooper B, Park S, Wood TC, Mao L, Quail P, Wing R, Dean R, Yu Y, Zharkikh A, Shen R, Sahasrabudhe S, Thomas A, Cannings R, Gutin A, Pruss D, Reid J, Tavtigian S, Mitchell J, Eldredge G, Scholl T, Miller RM, Bhatnagar S, Adey N, Rubano T, Tusneem N, Robinson R, Feldhaus J, Macalma T, Oliphant A, Briggs S: A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 2002, 296(5565):92-100.
3. Yu J, Hu S, Wang J, Wong GK, Li S, Liu B, Deng Y, Dai L, Zhou Y, Zhang X, Cao M, Liu J, Sun J, Tang J, Chen Y, Huang X, Lin W, Ye C, Tong W, Cong L, Geng J, Han Y, Li L, Li W, Hu G, Huang X, Li W, Li J, Liu Z, Li L, Liu J, Qi Q, Liu J, Li L, Li T, Wang X, Lu H, Wu T, Zhu M, Ni P, Han H, Dong W, Ren X, Feng X, Cui P, Li X, Wang H, Xu X, Zhai W, Xu Z, Zhang J, He S, Zhang J, Xu J, Zhang K, Zheng X, Dong J, Zeng W, Tao L, Ye J, Tan J, Ren X, Chen X, He J, Liu D, Tian W, Tian C, Xia H, Bao Q, Li G, Gao H, Cao T, Wang J, Zhao W, Li P, Chen W, Wang X, Zhang Y, Hu J, Wang J, Liu S, Yang J, Zhang G, Xiong Y, Li Z, Mao L, Zhou C, Zhu Z, Chen R, Hao B, Zheng W, Chen S, Guo W, Li G, Liu S, Tao M, Wang J, Zhu L, Yuan L, Yang H: A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 2002, 296(5565):79-92.
4. Alonso-Blanco C, Koornneef M: Naturally occurring variation in Arabidopsis: An underexploited resource for plant genetics. Trends in Plant Science 2000, 5(1):22-29.
5. Nordborg M, Hu TT, Ishino Y, Jhaveri J, Toomajian C, Zheng H, Bakker E, Calabrese P, Gladstone J, Goyal R, Jakobsson M, Kim S, Morozov Y, Padhukasahasram B, Plagnol V, Rosenberg NA, Shah C, Wall JD, Wang J, Zhao K, Kalbfleisch T, Schulz V, Kreitman M, Bergelson J: The pattern of polymorphism in Arabidopsis thaliana. PLoS Biol 2005, 3(7):e196.
6. Wright SI, Bi IV, Schroeder SG, Yamasaki M, Doebley JF, McMullen MD, Gaut BS: The effects of artificial selection on the maize genome. Science 2005, 308(5726):1310-1314.
7. Tanksley SD, McCouch SR: Seed banks and molecular maps: unlocking genetic potential from the wild. Science 1997, 277(5329):1063- 1066.
8. Falush D, Stephens M, Pritchard JK: Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 2003, 164(4):1567-1587.
9. Pritchard JK, Stephens M, Donnelly P: Inference of population structure using multilocus genotype data. Genetics 2000, 155(2):945-959.
10. Brown AHD: The case for core collection. Genome 1989, 31:818-824.
11. Schoen DJ, Brown AHD: Conservation of allelic richness in wild crop relatives is aided by assessment of genetic markers. Proceedings of the National Academy of Sciences of the United States of America 1993, 90(22):10623-10627.
12. Bataillon TM, David JL, Schoen DJ: Neutral genetic markers and conservation genetics: Simulated germplasm collections. Genetics 1996, 144(1):409-417.
13. McKhann HI, Camilleri C, Berard A, Bataillon T, David JL, Reboud X, Le Corre V, Caloustian C, Gut IG, Brunel D: Nested core collections maximizing genetic diversity in Arabidopsis thaliana. Plant J 2004, 38(1):193-202.
14. Cook DR: Medicago truncatula - a model in the making! Curr Opin Plant Biol 1999, 2(4):301-304.
15. The Medicago Handbook. [http://www.noble.org/Medicago-Handbook/]. .
16. Young ND, Cannon SB, Sato S, Kim D, Cook DR, Town CD, Roe BA, Tabata S: Sequencing the genespaces of Medicago truncatula and Lotus japonicus. Plant Physiol 2005, 137(4):1174-1181.
17. Ane JM, Kiss GB, Riely BK, Penmetsa RV, Oldroyd GE, Ayax C, Levy J, Debelle F, Baek JM, Kalo P, Rosenberg C, Roe BA, Long SR, Denarie J, Cook DR: Medicago truncatula DMI1 required for bacterial and fungal symbioses in legumes. Science 2004, 303(5662):1364-1367.
18. Endre G, Kereszt A, Kevei Z, Mihacea S, Kalo P, Kiss GB: A receptor kinase gene regulating symbiotic nodule development. Nature 2002, 417(6892):962-966.
19. Levy J, Bres C, Geurts R, Chalhoub B, Kulikova O, Duc G, Journet EP, Ane JM, Lauber E, Bisseling T, Denarie J, Rosenberg C, Debelle F: A putative Ca2+ and calmodulin-dependent protein kinase required for bacterial and fungal symbioses. Science 2004, 303(5662):1361-1364.
20. Limpens E, Franken C, Smit P, Willemse J, Bisseling T, Geurts R: LysM domain receptor kinases regulating rhizobial Nod factor-induced infection. Science 2003, 302(5645):630-633.
21. Stacey G, Libault M, Brechenmacher L, Wan J, May GD: Genetics and functional genomics of legume nodulation. Curr Opin Plant Biol 2006, 9(2):110-121.
22. Bonnin I, Prosperi JM, Olivieri I: Genetic markers and quantitative genetic variation in Medicago truncatula (Leguminosae): a comparative analysis of population structure. Genetics 1996, 143(4):1795-1805.
23. Bonnin I, Ronfort J, Wozniak F, Olivieri I: Spatial effects and rare outcrossing events in Medicago truncatula (Fabaceae). Mol Ecol 2001, 10(6):1371-1383.
24. Ellwood SR, D'Souza NK, Kamphuis LG, Burgess TI, Nair RM, Oliver RP: SSR analysis of the Medicago truncatula SARDI core collection reveals substantial diversity and unusual genotype dispersal throughout the Mediterranean basin. Theor Appl Genet 2006:1-7.
25. Thuillet AC, Bataillon T, Poirier S, Santoni S, David JL: Estimation of long-term effective population sizes through the history of durum wheat using microsatellite data. Genetics 2005, 169(3):1589-1599.
26. Ostrowski MF, David J, Santoni S, McKhann H, Reboud X, Le Corre V, Camilleri C, Brunel D, Bouchez D, Faure B, Bataillon T: Evidence for a large-scale population structure among accessions of Arabidopsis thaliana: possible causes and consequences for the distribution of linkage disequilibrium. Molecular Ecology 2006, 15(6):1507-1517.
27. Bonnin I, Huguet T, Gherardi M, Prosperi JM, Olivieri I: High level of polymorphism and spatial structure in a selfing plant species, Medicago truncatula (Leguminosae), shown using RAPD markers. Am J Bot 1996, 83:843-855.
28. Ohta T: Linkage disequilibrium due to random genetic drift in finite subdivided populations. Proc Natl Acad Sci U S A 1982, 79(6):1940-1944.
29. Wakeley J, Lessard S: Theory of the Effects of Population Structure and Sampling on Patterns of Linkage Disequilibrium Applied to Genomic Data From Humans. Genetics 2003, 164(3):1043-1053.
30. Evanno G, Regnaut S, Goudet J: Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 2005, 14(8):2611-2620.
31. Comes HP and Kadereit, J.W.: The effects of quaternary climatic changes on plant distribution and evolution. Trends in Plant Science 1998, 3:432-438.
32. Hewitt GM: Genetic consequences of climatic oscillations in the Quaternary. Philos Trans R Soc Lond B Biol Sci 2004, 359(1442):183-95; discussion 195.
33. Petit RJ, Pineau E, Demesure B, Bacilieri R, Ducousso A, Kremer A: Chloroplast DNA footprints of postglacial recolonization by oaks. Proceedings of the National Academy of Sciences of the United States of America 1997, 94(18):9996-10001.
34. Zaharieva M, Santoni S, David J: Use of RFLP markers to study genetic diversity and to build a core-collection of the wild wheat relative Ae. geniculata Roth (= Ae. ovata). Genetics Selection Evolution 2001, 33 (Suppl 1):S269-S288.
35. Baquerizo-Audiot E, Desplanque B, Prosperi JM, S. S: Characterization of microsatellite loci in the diploid legume Medicago truncatula (barrel medic). Molecular Ecology Notes 2001, 1(1-2):1-3.
36. Belkhir K., Borsa P., Chikhi L., N. R, F. B: GENETIX 4.05, logiciel sous Windows TM pour la génétique des populations. . 1996-2004
37. Raymond M, Rousset F: GENEPOP (Version 1.2): Population genetics software for exact tests and ecumenicism. Journal of Heredity 1995, 86(3):248-249.
38. Hardy O, Vekemans X: Spagedi: a versatile computer program to analyse spatial genetic structure at the individual or population levels. Molecular Ecology Notes 2002, 2(618-620):.
39. Weir BS, Cockerham CC: Estimating F-statistics for the analysis of population sructure. Evolution 1984, 38:1358-1370.
40. Gouesnard B, Bataillon TM, Decoux G, Rozale C, Schoen DJ, David JL: MSTRAT: an algorithm for building germ plasm core collections by maximizing allelic or phenotypic richness. J Hered 2001, 92(1):93-94.
41. MSTRAT: Software v4.1. [http://www.montpellier.inra.fr/gap/MSTRAT/ mstratno.htm]. .
42. Wolfram S: Mathematica: a system for doing mathematics by computer. Paris , Addison-Wesley; 1991.