Comparative mapping among subsection Australes (genus Pinus, family Pinaceae)

Genome

Volumn 51, Issue 5, 2008, Pages 320-331

  Shepherd, Mervyn ^a   Williams, Claire G ^b  

^a SOUTHERN CROSS UNIVERSITY   (Australia)

^b DUKE UNIVERSITY   (United States)

Author keywords

Conifers; Gymnosperms; Map shrinkage; Meiosis; Microsatellites; Synteny

Indexed keywords

MICROSATELLITE DNA;

ARTICLE; CHROMOSOME MAP; COMPARATIVE STUDY; CROSS BREEDING; GENETIC LINKAGE; GENETIC MARKER; GENETIC POLYMORPHISM; GENETIC RECOMBINATION; GENETICS; GENOME; MEIOSIS; MOLECULAR EVOLUTION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PINE; SPECIES DIFFERENCE; SYNTENY;

BASE SEQUENCE; CHROMOSOME MAPPING; CROSSES, GENETIC; EVOLUTION, MOLECULAR; GENETIC MARKERS; GENOME, PLANT; LOD SCORE; MEIOSIS; MICROSATELLITE REPEATS; MOLECULAR SEQUENCE DATA; PINUS; POLYMORPHISM, GENETIC; RECOMBINATION, GENETIC; SPECIES SPECIFICITY; SYNTENY;

CONIFEROPHYTA; GYMNOSPERMAE; PINACEAE; PINUS (SUBGENUS); PINUS CARIBAEA VAR. HONDURENSIS; PINUS ELLIOTTII VAR. ELLIOTTII;

EID: 44449130401     PISSN: 08312796     EISSN: None     Source Type: Journal    
DOI: 10.1139/G08-018     Document Type: Article

References (69)

1. Adams, D.C., and Jackson, J.F. 1997. A phylogenetic analysis of the southern pines (Pinus subsection Australes Loudon) - biogeographical and ecological implications. Proc. Biol. Soc. Wash. 110: 681-692.
2. Amos, W. 2006. The hidden value of missing genotypes. Mol. Biol. Evol. 23: 1995-1996. doi:10.1093/molbev/msl078. PMID: 16891378.
3. Auckland, L.D., Bui, T., Zhou, Y., Shepherd, M., and Williams, C.G. 2002. Conifer microsatellite handbook. Corporate Press, Raleigh, N.C.
4. Axelrod, D.I. 1986. Cenozoic history of some western American pines. Ann. Mo. Bot. Gard. 73: 565-641. doi:10.2307/2399194.
5. Bousquet, J., Simon, L., and Lalonde, M. 1990. DNA amplification from vegetative and sexual tissues of trees using polymerase chain reaction. Can. J. For. Res. 20: 254-257. doi:10.1139/x90-037.
6. Brandham, P.E., and Doherty, M.-J. 1998. Genome size variation in the Aloaceae, an angiosperm family displaying karyotypic orthoselection. Ann. Bot. (Lond.), 82: 67-73. doi:10.1006/anbo.1998.0742.
7. Critchfield, W.B., and Little, E. 1966. Geographic distribution of the pines of the world. USDA Forest Service, Miscellaneous Publication No. 991. Washington, D.C.
8. Devey, M.E., Fiddler, T.A., Liu, B.H., Knapp, S.J., and Neale, D.B. 1994. An RFLP linkage map for loblolly pine based on a three-generation outbred pedigree. Theor. Appl. Genet. 88: 273-278. doi:10.1007/BF00223631.
9. Dvorak, W.S., Jordan, A.P., Hodge, G.P., and Romero, J.L. 2000. Assessing evolutionary relationships of pines in the Oocarpae and Australes subsections using RAPD markers. New For. 20: 163-192.
10. Echt, C.S., and Burns, R. 1999. SSRs derived from Pinus taeda ESTs [online]. Available from http://dendrome.ucdavis.edu/dendrome_genome/ssr-est. html [accessed 21 March 2008].
11. Eckert, A.J., and Hall, B.D. 2006. Phylogeny, historical biogeography, and patterns of diversification for Pinus (Pinaceae): phylogenetic tests of fossil-based hypotheses. Mol. Phylogenet. Evol. 40: 166-182. doi:10.1016/j.ympev.2006.03.009. PMID:16621612.
12. Ehrlich, J., Sankoff, D., and Nadeau, J.H. 1997. Synteny conservation and chromosomal rearrangements during mammalian evolution. Genetics, 147: 289-296. PMID:9286688.
13. Elsik, C.G., Minihan, V.T., Hall, S.E., Scarpa, A.M., and Williams, C.G. 2000. Low-copy microsatellite markers for Pinus taeda L. Genome, 43: 550-555. doi:10.1139/gen-43-3-550. PMID: 10902720.
14. Farjon, A., and Styles, B. 1997. Pinus (Pinaceae). Flora Neotropica Monograph 75. The New York Botanical Garden, New York.
15. Fisher, P.J., Richardson, T.E., and Gardner, R.C. 1998. Characteristics of single- and multi-copy microsatellites from Pinus radiata. Theor. Appl. Genet. 96: 969-979. doi:10.1007/s001220050828.
16. Gaut, B.S., and Doebley, J.F. 1997. DNA sequence evidence for the segmental allotetraploid origin of maize. Proc. Natl. Acad. Sci. U.S.A. 94: 6809-6814. doi:10.1073/pnas.94.13.6809. PMID:11038553.
17. Greenbaum, I.F., and Reed, M.J. 1984. Evidence for heterosynaptic pairing of the inverted segment in pericentric inversion heterozygotes of the deer mouse (Permyscus maniculatus). Cytogenet. Cell Genet. 38: 106-111. PMID:6467983.
18. Griffiths, A.J.F., Miller, J.H., Suzuki, D.T., Lewontin, R.C., and Gelbart, W.M. 2000. An introduction to genetic analysis. 7th ed. W.H. Freeman and Co., New York.
19. Hall, S.E., Dvorak, W.S., Johnston, J.S., Price, H.J., and Williams, C.G. 2000. Flow cytometric analysis of DNA content for tropical and temperate New World pines. Ann. Bot. (Lond.), 86: 1081-1086. doi:10.1006/anbo.2000. 1272.
20. Hicks, M., Adams, D., O'Keefe, S., Macdonald, E., and Hodgetts, R. 1998. The development of RAPD and microsatellite markers in lodgepole pine (Pinus contorta var. latifolia). Genome, 41: 797-805. doi:10.1139/gen-41-6-797.
21. Joyner, K.L., Wang, X.-R., Johnston, J.S., Price, H.J., and Williams, C.G. 2001. DNA content for Asian pines parallels New World relatives. Can. J. Bot. 79: 192-196. doi:10.1139/cjb-79-2-192.
22. Kirkpatrick, M., and Barton, N. 2006. Chromosome inversions, local adaptation and speciation. Genetics, 173: 419-434. doi:10.1534/genetics. 105.047985. PMID:16204214.
23. Komulainen, P., Brown, G.R., Mikkonen, M., Karhu, A., Garcia-Gil, M.R., O'Malley, D., et al. 2003. Comparing EST-based genetic maps between Pinus sylvestris and P. taeda. Theor. Appl. Genet. 107: 667-678. doi:10.1007/s00122-003-1312-2. PMID: 12827250.
24. Korol, A.B., Preygel, I.A., and Preygel, S.I. 1994. Recombination variation and evolution. 1st ed. Chapman and Hall, London.
25. Krupkin, A.B., Liston, A., and Strauss, S.H. 1996. Phylogenetic analysis of the hard pines (Pinus subgenus Pinus, Pinaceae) from chloroplast DNA restriction site analysis. Am. J. Bot. 83: 489-498. doi:10.2307/2446218.
26. Krutovsky, K.V., Troggio, M., Brown, G.R., Jermstad, K.D., and Neale, D.B. 2004. Comparative mapping in the Pinaceae. Genetics, 168: 447-461. doi:10.1534/genetics.104.028381. PMID:15454556.
27. Lagercrantz, U. 1998. Comparative mapping between Arabidopsis thaliana and Brassica nigra indicates that Brassica genomes have evolved through extensive genome replication accompanied by chromosome fusions and frequent rearrangements. Genetics, 150: 1217-1228. PMID:9799273.
28. Lander, E.S., Green, P., Abrahamson, J., Barlow, A., Daley, M.J., Lincoln, S.E., and Newburg, L. 1987. MAPMAKER: An interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics, 1: 174-181. doi:10.1016/0888-7543(87)90010-3. PMID:3692487.
29. Levin, D.A., and Wilson, A.C. 1976. Rates of evolution in seed plants: net increase in diversity of chromosome numbers and species numbers through time. Proc. Natl. Acad. Sci. U.S.A. 73: 2086-2090. doi:10.1073/pnas.73.6. 2086. PMID:16592327.
30. Liston, A., Robinson, W.A., Pinero, D., and Alvarez-Buylla, E.R. 1999. Phylogenetics of Pinus (Pinaceae) based on nuclear ribosomal DNA internal transcribed spacer region sequences. Mol. Phylogenet. Evol. 11: 95-100. doi:10.1006/mpev.1998.0550. PMID:10082614.
31. Little, E.L. 1971. Atlas of United States trees. Conifers and important hardwoods. USDA Forest Service, Miscellaneous Publication 1146. Washington, D.C.
32. Little, E.L., and Critchfield, W.B. 1969. Subdivisions of the genus Pinus. USDA Forest Service Miscellaneous Publication 144. Washington, D.C.
33. McWilliam, J.R. 1959. Interspecific incompatibility in Pinus. Am. J. Bot. 46: 425-433. doi:10.2307/2439138.
34. Millar, C.I. 1993. Impact of the Eocene on the evolution of Pinus L. Ann. Mo. Bot. Gard. 80: 471-498. doi:10.2307/2399795.
35. Millar, C.I. 1998. Early evolution of pines. In Ecology and biogeography of Pinus. Edited by D.M. Richardson. Cambridge University Press, Cambridge, U.K. pp. 69-87.
36. Mirov, N.T. 1967. The genus Pinus. The Ronald Press Company, New York.
37. Mirov, N.T., Frank, E., and Zavarin, E. 1965. Chemical composition of P. elliottii var. elliottii turpentine and its possible relation to taxonomy of several pine species. Phytochemistry, 4: 563-568. doi:10.1016/S0031-9422(00)86217-2.
38. Morton, N.E. 1956. The detection and estimation of linkage between genes for elliptocytosis and the Rh blood type. Am. J. Hum. Genet. 8: 80-96. PMID:13313518.
39. Murray, B.G. 1998. Nuclear DNA amounts in gymnosperms. Ann. Bot. (Lond.), 82(Suppl. A): 3-15. doi:10.1006/anbo.1998.0764.
40. Nelson, C.D., Nance, W.L., and Wagner, D.B. 1994. Chloroplast DNA variation among and within taxonomic varieties of Pinus caribaea and Pinus elliottii. Can. J. For. Res. 24: 424-426. doi:10.1139/x94-057.
41. Nicholas, K.B., and Nicholas, H.J. 1997. GeneDoc: a tool for editing and annotating multiple sequence alignments [computer program]. Available from the National Resource for Biomedical Supercomputing at www.psc.edu/biomed/genedoc/ [verified 8 March 2007].
42. Noor, M.A.F., Grams, K.L., Bertucci, L.A., and Reiland, J. 2001. Chromosomal inversions and the reproductive isolation of species. Proc. Natl. Acad. Sci. U.S.A. 98: 12084-12088. doi:10.1073/pnas.221274498. PMID:11593019.
43. Paterson, A.H. 1996. Genome mapping in plants. Academic Press, San Diego, Calif.
44. Pelgas, B., Bousquet, J., Beauseigel, S., and Isabel, N. 2005. A composite linkage map from two crosses for the species complex Picea mariana x Picea rubens and analysis of synteny with other Pinaceae. Theor. Appl. Genet. 111: 1466-1488. doi:10.1007/s00122-005-0068-2. PMID:16215729.
45. Reinisch, A.J., Dong, J., Brubaker, C.L., Stelly, D.M., Wendel, J.F., and Paterson, A.H. 1994. A detailed RFLP map of cotton, Gossypium hirsutum x G. barbadense - chromosome organization and evolution in a disomic polyploid genome. Genetics, 138: 829-847. PMID:7851778.
46. Rieseberg, L.H. 2001. Chromosomal rearrangements and speciation. Trends Ecol. Evol. 16: 351-358. doi:10.1016/S0169-5347(01)02187-5. PMID:11403867.
47. Rieseberg, L.H., Baird, S.J.E., and Gardner, K.A. 2000. Hybridisation, introgression, and linkage evolution. Plant Mol. Biol. 42: 205-224. doi:10.1023/A:1006340407546. PMID:10688138.
48. Righter, F.I., and Duffield, J.W. 1951. Interspecies hybrids in pines: a summary of interspecific crosses in the genus Pinus made at the Institute of Forest Genetics. J. Hered. 42: 75-80. PMID:14832455.
49. Sax, K. 1960. Meiosis in interspecific pine hybrids. For. Sci. 6: 135-138.
50. Sax, K., and Sax, H.J. 1933. Chromosome number and morphology in the conifers. J. Arnold Arbor. Harv. Univ. 14: 356-374.
51. Saylor, C.L., and Smith, B.W. 1966. Meiotic irregularity in species and interspecific hybrids of Pinus. Am. J. Bot. 53: 453-468. doi:10.2307/2440344.
52. Shepherd, M., Cross, M., Maguire, T., Dieters, M.J., Williams, C.G., and Henry, R.J. 2002. Transpecific microsatellites for hard pines. Theor. Appl. Genet. 104: 819-827. doi:10.1007/s00122-001-0794-z. PMID:12582642.
53. Shepherd, M., Huang, S., Eggler, P., Cross, M., Dale, G.T., Dieters, M.J., and Henry, R.J. 2006. Congruence in QTL for adventitious rooting in unrelated outbred and inbred-like Pinus elliottii x P. caribaea hybrids resolves between and within species effects. Mol. Breed. 18: 11-28. doi:10.1007/s11032-006-9006-5.
54. Smith, D.N., and Devey, M.E. 1994. Occurrence and inheritance of microsatellites in Pinus radiata. Genome, 37: 977-983. doi:10.1139/g94-138. PMID:7828844.
55. Soranzo, N., Provan, J., and Powell, W. 1998. Characterization of microsatellite loci in Pinus sylvestris L. Mol. Ecol. 7: 1247-1263. doi:10.1046/j.1365-294x.1998.00406.x. PMID:9734079.
56. Stebbins, G.L. 1945. The cytological analysis of species hybrids. II. Bot. Rev. 11: 463-486.
57. Stephens, S.G. 1950. The internal mechanism of speciation in Gossypium. Bot. Rev. 56: 115-149.
58. Syring, J., Willyard, A., Cronn, R., and Liston, A. 2006. Evolutionary relationships among Pinus (Pinaceae) subsections inferred from multiple low-copy nuclear loci. Am. J. Bot. 92: 2086-2100.
59. Tanksley, S.D., Ganal, M.W., Prince, J.P., de Vicente, M.C., Bonierbale, M.W., Broun, P., et al. 1992. High density molecular linkage maps of the tomato and potato genomes. Genetics, 132: 1141-1160. PMID:1360934.
60. Van Ooijen, J., and Voorrips, R. 2001. JoinMap 3.0. Software for the calculation of genetic linkage maps. Release 3. Plant Research International B.V., Wageningen, the Netherlands.
61. Voorrips, R. 2001. MapChart version 2.0: Windows software for the graphical presentation of linkage groups and QTLs. Release 2.0. Plant Research International B.V., Wageningen, the Netherlands. Wakamiya, I., Newton, R.J., Johnston, J.S., and Price, H.J. 1993.
62. Genome size and environmental factors in the genus Pinus. Am. J. Bot. 80: 1235-1241. doi:10.2307/2445706.
63. Weir, B.S. 1990. Genetic data analysis: methods for discrete population genetic data. Sinauer Associates, Sunderland, Mass.
64. Wendel, J.F. 1989. New World tetraploid cottons contain Old World cytoplasm. Proc. Natl. Acad. Sci. U.S.A. 86: 4132-4136. doi:10.1073/pnas.86.11.4132. PMID:16594050.
65. Whitkus, R., Doebley, J., and Lee, M. 1992. Comparative genome mapping of sorghum and maize. Genetics, 132: 1119-1130. PMID:1360933.
66. Williams, C.G., Joyner, K.L., Auckland, L.D., Johnston, S., and Price, H.J. 2002. Genomic consequences of interspecific Pinus spp. hybridisation. Biol. J. Linn. Soc. 75: 503-508. doi:10.1046/j.1095-8312. 2002.00038.x.
67. Zamir, D., and Tadmor, Y. 1986. Unequal segregation of nuclear genes in plants. Bot. Gaz. 147: 355-358. doi:10.1086/337602.
68. Zhou, Y., Bui, T., Auckland, L.D., and Williams, C.G. 2002. Undermethylated DNA as a source of microsatellites from a conifer genome. Genome, 45: 91-99. doi:10.1139/g01-119. PMID: 11908673.
69. Zhou, Y., Gwaze, D.P., Reyes-Valdés, M.H., Bui, T., and Williams, C.G. 2003. No clustering for linkage map based on low-copy and undermethylated microsatellites. Genome, 46: 809-816. doi:10.1139/g03-062. PMID:14608397.