Relationships among diploid members of the medicago sativa (fabaceae) species complex based on chloroplast and mitochondrial DNA sequences

Systematic Botany

Volumn 35, Issue 1, 2010, Pages 140-150

  Havananda, Tee ^a   Brummer, E Charles ^b   Maureira Butler, Iván J ^c   Doyle, Jeff J ^a  

^a Cornell University ^*  (United States)

^b UNIVERSITY OF GEORGIA   (United States)

^c Agri Aquaculture Nutritional Genomic Center (CGNA)   (Chile)

Author keywords

Chloroplast DNA; Medicago; Mitochondrial DNA; Statistical parsimony

Indexed keywords

FABACEAE; MEDICAGO; MEDICAGO SATIVA;

EID: 77749304309     PISSN: 03636445     EISSN: 15482324     Source Type: Journal    
DOI: 10.1600/036364410790862506     Document Type: Article

References (84)

1. Adams, K.L. 2007. Evolution of duplicate gene expression in polyploid and hybrid plants. The Journal of Heredity 98: 136-141.
2. Adams, K.L. and J.F. Wendel. 2005. Novel patterns of gene expression in polyploid plants. Trends in Genetics 21: 539-543.
3. Ballard, J.W.O. and M.C. Whitlock. 2004. The incomplete natural history of mitochondria. Molecular Ecology 13: 729-744.
4. Bauchan, G.R. and M.A. Hossain. 1997. Karyotypic analysis of C-banded chromosomes of diploid alfalfa: Medicago sativa ssp. caerulea and ssp. falcata and their hybrid. The Journal of Heredity 88: 533-537.
5. Baum, D.A. 2009. Species as ranked taxa. Systematic Biology 58: 74-86.
6. Bena, G. 2001. Molecular phylogeny supports the morphologically based taxonomic transfer of the "medicoid" Trigonella species to the genus Medicago L. Plant Systematics and Evolution 229: 217-236.
7. Bena, G., M.-F. Jubier, I. Olivieri, and B. Lejeune. 1998a. Ribosomal external and internal transcribed spacers: combined use in the phylogenetic analysis of Medicago (Leguminosae). Journal of Molecular Evolution 46: 299-306.
8. Bena, G., B. Lejeune, J.-M. Prosperi, and I. Olivieri. 1998b. Molecular phylogenetic approach for studying life-history evolution: the ambiguous example of the genus Medicago L. Proceedings of the Royal Society B: Biological Sciences 265: 1141-1151.
9. Bena, G., J.-M. Prosperi, B. Lejeune, and I. Olivieri. 1998c. Evolution of annual species of the genus Medicago: a molecular phylogenetic approach. Molecular Phylogenetics and Evolution 9: 552-559.
10. Bingham, E.T. and T.J. McCoy. 1979. Cultivated alfalfa at the diploid level: origin, reproductive stability, and yield of seed and forage. Crop Science 19: 97-100.
11. Boe, A., R. Bortnem, K.F. Higgins, A.D. Kruse, K.D. Kephart, and S. Selman. 1998. Breeding yellow-flowered alfalfa for combined wildlife habitat and forage purposes. South Dakota Agricultural Experiment Station Bulletin 727. Brookings: South Dakota State University.
12. Brummer, E.C. 2004. Genomics research in alfalfa, Medicago sativa L. Pp. 110-142 in Legume crop genomics, eds. R.F. Wilson, H.T. Stalker, and E.C. Brummer. Champaign, Illinois: AOCS Press.
13. Brummer, E.C., P. Cazcarro, and D. Luth. 1999. Ploidy determination of alfalfa germplasm accessions using flow cytometry. Crop Science 39: 1202-1207.
14. Brummer, E.C., G. Kochert, and J.H. Bouton. 1991. RFLP variation in diploid and tetraploid alfalfa. Theoretical and Applied Genetics 83: 89-96.
15. Chan, K.M.A. and S.A. Levin. 2005. Leaky prezygotic isolation and porous genomes: rapid introgression of maternally inherited DNA. Evolution 59: 720-729.
16. Clark, A.G. 1990. Inference of haplotypes from PCR-amplified samples of diploid populations. Molecular Biology and Evolution 7: 111-122.
17. Clement, M., D. Posada, and K. Crandall. 2000. TCS: a computer program to estimate gene genealogies. Molecular Ecology 9: 1657-1659.
18. Comai, L. 2005. The advantages and disadvantages of being polyploid. Nature Reviews Genetics 6: 836-846.
19. Demesure, B., N. Sodzi, and R. J. Petit. 1995. A set of universal primers for amplification of polymorphic non-coding regions of mitochondrial and chloroplast DNA in plants. Molecular Ecology 4: 129-131.
20. de Queiroz, K. 2007. Species concepts and species delimitation. Systematic Biology 56: 879-886.
21. Diwan, N., A.A. Bhagwat, G.B. Bauchan, and P.B. Cregan. 1997. Simple sequence repeat DNA markers in alfalfa and perennial and annual Medicago species. Genome 40: 887-895.
22. Downie, S.R., D.S. Katz-Downie, E.J. Rogers, H.L. Zujewski, and E. Small. 1998. Multiple independent losses of the plastid rpoC1 intron in Medicago (Fabaceae) as inferred from phylogenetic analyses of nuclear ribosomal DNA internal transcribed spacer sequences. Canadian Journal of Botany 76: 791-803.
23. Doyle, J.J. and J.L. Doyle. 1987. Arapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemical Bulletin 19: 11-15.
24. Doyle, J.J., J.I. Davis, R.J. Soreng, D. Garvin, and M.J. Anderson. 1992. Chloroplast DNA inversions and the origin of the grass family (Poaceae). Proceedings of the National Academy of Sciences USA 89: 7722-7726.
25. Doyle, J.J., J.L. Doyle, J.T. Rauscher, and A.H.D. Brown. 2004. Evolution of the perennial soybean polyploid complex (Glycine subgenus Glycine): a study of contrasts. Biological Journal of the Linnean Society 82: 583-597.
26. Doyle, J.J., M. Morgante, S.V. Tingey, and W. Powell. 1998. Size homoplasy in chloroplast microsatellites of wild perennial relatives of soybean (Glycine subgenus Glycine). Molecular Biology and Evolution 15: 215 - 218.
27. Dubcovsky, J. and J. Dvorak. 2007. Genome plasticity a key factor in the success of polyploid wheat under domestication. Science 316: 1862-1866.
28. Ellstrand, N.C., H.C. Prentice, and J.F. Hancock. 1999. Gene flow and introgression from domesticated plants into their wild relatives. Annual Review of Ecology and Systematics 30: 539-563.
29. Excoffier, L., G. Laval, and S. Schneider. 2005. Arlequin ver. 3.0: an integrated software package for population genetics data analysis. Evolutionary Bioinformatics Online 1: 47-50.
30. Falahati-Anbaran, M., A.A. Habashi, M. Esfahany, S.A. Mohammadi, and B. Ghareyazie. 2007. Population genetic structure based on SSR markers in alfalfa (Medicago sativa L.) from various regions contiguous to the centres of origin of the species. Journal of Genetics 86: 59-63.
31. Forsthoefel, N.R., H.J. Bohnert, and S.E. Smith. 1992. Discordant inheritance of mitochondrial and plastid DNA in diverse alfalfa genotypes. The Journal of Heredity 83: 342-345.
32. Gaeta, R.T., J.C. Pires, F. Iniguez-Luy, E. Leon, and T.C. Osborn. 2007. Genomic changes in resynthesized Brassica napus and their effect on gene expression and phenotype. The Plant Cell 19: 3403-3417.
33. Ghérardi, M., B. Mangin, B. Goffinet, D. Bonnet, and T. Huguet. 1998. A method to measure genetic distance between allogamous populations of alfalfa (Medicago sativa) using RAPD molecular markers. Theoretical and Applied Genetics 96: 406-412.
34. Gondo, T., S. Sato, K. Okumura, S. Tabata, R. Akashi, and S. Isobe. 2007. Quantitative trait locus analysis of multiple agronomic traits in the model legume Lotus japonicus. Genome 50: 627-637.
35. Hamilton, M.B. 1999. Four primer pairs for the amplification of chloro-plast intergenic regions with intraspecific variation. Molecular Ecology 8: 521-523.
36. Johnson, L.B. and J.D. Palmer. 1989. Heteroplasmy of chloroplast DNA in Medicago. Plant Molecular Biology 12: 3-11.
37. Kaló, P., G. Endre, L. Zimányi, G. Csanádi, and G.B. Kiss. 2000. Construction of an improved linkage map of diploid alfalfa (Medicago sativa). Theoretical and Applied Genetics 100: 641-657.
38. Kidwell, K.K., D.F. Austin, and T.C. Osborn. 1994. RFLP evaluation of nine Medicago accessions representing the original germplasm sources for North-American alfalfa cultivars. Crop Science 34: 230 - 236.
39. Kiss, G.B., G. Csanádi, K. Kálmán, P. Kaló, and L. Ökrész. 1993. Construction of a basic genetic map for alfalfa using RFLP, RAPD, isozyme and morphological markers. Molecular and General Genetics 238: 129-137.
40. Lesins, K. 1962. Interspecific crosses involving alfafa. III. Medicago sativa L. × M. prostrata Jacq. Canadian Journal of Genetics and Cytology 4: 14-23.
41. Lesins, K. 1968. Interspecific crosses involving alfalfa. IV. Medicago glomerata × M. sativa with reference to M. prostrata. Canadian Journal of Genetics and Cytology 10: 536-544.
42. Lesins, K. 1969. Relationship of taxa in genus Medicago as revealed by hybridization. IV. M. hybrida × M. suffruticosa. Canadian Journal of Genetics and Cytology 11: 340-345.
43. Lesins, K.A. and I. Lesins. 1979. Genus Medicago (Leguminosae): a taxogenetic study. The Hague: Dr. W. Junk bv Publishers.
44. Martinsen, G.D., T.G. Whitham, R.J. Turek, and P. Keim. 2001. Hybrid populations selectively filter gene introgression between species. Evolution 55: 1325-1335.
45. Masoud, S.A., L.B. Johnson, and E.L. Sorensen. 1990. High transmission of paternal plastid DNA in alfalfa plants demonstrated by restriction fragment polymorphic analysis. Theoretical and Applied Genetics 79: 49-55.
46. Maureira, I. J. 2004. Alfalfa (Medicago sativa subsp. sativa) population improvement: genetic diversity within and among Medicago species and trait-associations with molecular markers. Ph. D. thesis. Madison: University of Wisconsin.
47. Maureira-Butler, I.J., B.E. Pfeil, A. Muangprom, T.C. Osborn, and J.J. Doyle. 2008. The reticulate history of Medicago (Fabaceae). Systematic Biology 57: 466-482.
48. McCoy, T.J. 1982. The inheritance of 2n pollen formation in diploid alfalfa Medicago sativa. Canadian Journal of Genetics and Cytology 24: 315-323.
49. McCoy, T.J. and E.T. Bingham. 1988. Cytology and cytogenetics of alfalfa. Pp. 737-776 in Alfalfa and alfalfa improvement, Agronomy monograph 29, ed. Hanson A.A., co-eds. D.K. Barnes and R.R. Hill, Jr. Madison, Wisconsin: ASA, CSSA, SSSA.
50. McGuire, J.A., C.W. Linkem, M.S. Koo, D.W. Hutchison, A.K. Lappin, D.I. Orange, J. Lemos-Espinal, B.R. Riddle, and J.R. Jaeger. 2007. Mitochondrial introgression and incomplete lineage sorting through space and time: phylogenetics of crotaphytid lizards. Evolution 61: 2879-2897.
51. Moore, W.S. 1995. Inferring phylogenies from mtDNA variation: mitochon-drial-gene trees versus nuclear-gene trees. Evolution 49: 718-726.
52. Muller, M.-H., C. Poncet, J.M. Prosperi, S. Santoni, and J. Ronfort. 2006. Domestication history in the Medicago sativa species complex: inferences from nuclear sequence polymorphism. Molecular Ecology 15: 1589-1602.
53. Muller, M.-H., J.M. Prosperi, S. Santoni, and J. Ronfort. 2001. How mitochondrial DNA diversity can help to understand the dynamics of wild-cultivated complexes. The case of Medicago sativa in Spain. Molecular Ecology 10: 2753-2763.
54. Muller, M.H., J.M. Prosperi, S. Santoni, and J. Ronfort. 2003. Inferences from mitochondrial DNA patterns on the domestication history of alfalfa (Medicago sativa). Molecular Ecology 12: 2187-2199.
55. Palmer, J.D. 1992. Mitochondrial DNA in plant systematics: applications and limitations. Pp. 36 - 49 in Molecular systematics of plants, eds. D. Soltis, P. Soltis, and J.J. Doyle. New York: Chapman and Hall.
56. Posada, D. and K.A. Crandall. 2001. Intraspecific gene genealogies: trees grafting into networks. Trends in Ecology & Evolution 16: 37-45.
57. Quiros, C.F. 1982. Tetrasomic segregation for multiple alleles in alfalfa. Genetics 101: 117-127.
58. Quiros, C.F. and G.R. Bauchan. 1988. The genus Medicago and the origin of the Medicago sativa complex. Pp. 93-124 in Alfalfa and alfalfa improvement, Agronomy monograph 29, ed. A.A. Hanson, co-eds. D.K. Barnes and R.R. Hill, Jr. Madison, Wisconsin: ASA, CSSA, SSSA.
59. Rieseberg, L.H. and D.E. Soltis. 1991. Phylogenetic consequences of cytoplasmic gene flow in plants. Evolutionary Trends in Plants 5: 65-84.
60. Rieseberg, L.H. and J.F. Wendel. 1993. Introgression and its consequences in plants. Pp. 70-109 in Hybrid zones and the evolutionary process, ed. R.G. Harrison. New York: Oxford University Press.
61. Rieseberg, L.H., J. Whitton, and C.R. Linder. 1996. Molecular marker incongruence in plant hybrid zones and phylogenetic trees. Acta Botanica Neerlandica 45: 243-262.
62. Rozas, J., J.C. Sánchez-Del Barrio, X. Messeguer, and R. Rozas. 2003. DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19: 2496-2497.
63. Schumann, C.M. and J.F. Hancock. 1989. Paternal inheritance of plastids in Medicago sativa. Theoretical and Applied Genetics 78: 863-866.
64. Segovia-Lerma, A., R.G. Cantrell, J.M. Conway, and I.M. Ray. 2003. AFLP-based assessment of genetic diversity among nine alfalfa germplasms using bulk DNA templates. Genome 46: 51-58.
65. Senjo, M., K. Kimura, Y. Watano, K. Ueda, and T. Shimizu. 1999. Extensive mitochondrial introgression from Pinus pumila to P. parviflora var. pentaphylla (Pinaceae). Journal of Plant Research 112: 97-105.
66. Simmons, M.P. and H. Ochoterena. 2000. Gaps as characters in sequence-based phylogenetic analyses. Systematic Biology 49: 369-381.
67. Skinner, D.Z. 2000. Non random chloroplast DNA hypervariablility in Medicago sativa. Theoretical and Applied Genetics 101: 1242-1249.
68. Small, E. and M. Jomphe. 1989. A synopsis of the genus Medicago (Leguminosae). Canadian Journal of Botany 67: 3260-3294.
69. Smith, S.E. 1989. Influence of parental genotype on plastid inheritance in Medicago sativa. The Journal of Heredity 80: 214-217.
70. Smith, S.E., E.T. Bingham, and R.W. Fulton. 1986. Transmission of chlorophyll deficiencies in Medicago sativa: evidence for biparental inheritance of plastids. The Journal of Heredity 77: 35-38.
71. Soltis, D.E., P.S. Soltis, J.C. Pires, A. Kovarik, J.A. Tate, and E. Mavrodiev. 2004a. Recent and recurrent polyploidy in Tragopogon (Asteraceae): cytogenetic, genomic and genetic comparisons. Biological Journal of the Linnean Society 82: 485-501.
72. Soltis, D.E., P.S. Soltis, D.W. Schemske, J.F. Hancock, J.N. Thompson, B.C. Husband, and W.S. Judd. 2007. Autopolyploidy in angiosperms: have we grossly underestimated the number of species? Taxon 56: 13-30.
73. Soltis, D.E., P.S. Soltis, and J.A. Tate. 2004b. Advances in the study of poly-ploidy since Plant Speciation. The New Phytologist 161: 173-191.
74. Soltis, P.S. and D.E. Soltis. 2000. The role of genetic and genomic attributes in the success of polyploids. Proceedings of the National Academy of Sciences USA 97: 7051-7057.
75. Stanford, E.H. 1951. Tetrasomic inheritance in alfalfa. Agronomy Journal 43: 222-225.
76. Steele, K.P. and M.F. Wojciechowski. 2003. Phylogenetic analyses of tribes Trifolieae and Vicieae, based on sequences of the plastid gene, matK (Papilionoideae: Leguminosae). Pp. 355-370 in Advances in legume systematics, part 10, Higher level systematics, eds. B.B. Klitgaard and A. Bruneau. Kew: Royal Botanic Garden.
77. *and other methods), v. 4.0 beta 10. Sunderland: Sinauer Associates.
78. Templeton, A.R., K.A. Crandall, and C.F. Sing. 1992. A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence data. III. Cladogram estimation. Genetics 132: 619-633.
79. Thoquet, P., M. Ghérardi, E.-P. Journet, A. Kereszt, J.-M. Ané, J.-M. Prosperi, and T. Huguet. 2002. The molecular genetic linkage map of the model legume Medicago truncatula: an essential tool for comparative legume genomics and the isolation of agronomically important genes. BMC Plant Biology 2: 1.
80. Tsutsui, K., A. Suwa, K. Sawada, T. Kato, T.A. Ohsawa, and Y. Watano. 2009. Incongruence among mitochondrial, chloroplast, and nuclear gene trees in Pinus subgenus Strobus (Pinaceae). Journal of Plant Research Online First. Advance online publication. Retrieved July 8, 2009. doi: 10.1007/s10265-009-0246-4.
81. Valizadeh, M., K.K. Kang, A. Kanno, and T. Kameya. 1996. Analysis of genetic distance among nine Medicago species by using DNA polymorphisms. Breeding Science 46: 7-10.
82. van der Niet, T. and H.P. Linder. 2008. Dealing with incongruence in the quest for the species tree: a case study from the orchid genus Satyrium Molecular Phylogenetics and Evolution 47: 154-174.
83. Wang, J., L. Tian, H.-S. Lee, N.E. Wei, H. Jiang, B. Watson, A. Madlung, T.C. Osborn, R.W. Doerge, L. Comai, and Z.J. Chen. 2006. Genomewide nonadditive gene regulation in Arabidopsis allotetra-ploids. Genetics 172: 507-517.
84. Wendel, J.F. 2000. Genome evolution in polyploids. Plant Molecular Biology 42: 225-249.