Theoretical and Applied Genetics

, Volume 93, Issue 4, pp 587–592 | Cite as

Inter- and intraspecific polymorphism at chloroplast SSR loci and the inheritance of plastids in Pinus radiata D. Don

  • S. A. Cato
  • T. E. Richardson


DNA sequence analysis of chloroplast genomes has revealed many short nucleotide repeats analogous to nuclear microsatellites, or simple sequence repeats (SSRs). We designed PCR primers flanking five of these regions identified in the chloroplast sequence from Pinus thunbergii and tested them for amplification in Pinus radiata, P. elliotii, P. taeda, P. strobus, Pseudotsuga menziesii, Cupressus macrocarpa, four New Zealand native conifer species (Podocarpus totara, Podocarpus hallii, Podocarpus nivalis, Agathis australis), and four angiosperms (Vitex lucens, Nestegis cunninghamii, Actinidia chinensis, and Arabidopsis thaliana). A PCR product in the expected size range was amplified from all species and interspecific polymorphism was detected at all five loci. Intraspecific polymorphism was detected in P. radiata with four of the five primer pairs. One of these polymorphic chloroplast SSR (cpSSR) was then used to determine the inheritance of chloroplasts in 206 progeny from four control-pollinated, full-sibling P. radiata families. Approximately 99% of the progeny had the cpSSR variant of the pollen parent indicating that in Pinus radiata, like most other conifers, chloroplasts are typically inherited from the paternal parent. These results suggest that polymorphic chloroplast SSRs will be a valuable tool for studying chloroplast diversity, cyto-nuclear disequilibrium, and plastid inheritance in a range of species, and for the analysis of gene flow via pollen and paternity in species with paternal transmission of chloroplasts.

Key words

Chloroplast DNA SSRs Pinus radiata Plastid inheritance 


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  1. Boscherini G, Morgante M, Rossi P, Vendramin GG (1994) Allozyme and chloroplast DNA variation in Italian and Greek populations of Pinus leucodermis. Heredity 73:284–290Google Scholar
  2. Chesnoy L, Thomas MJ (1971) Electron microscopy studies on gametogenesis and fertilization in gymnosperms. Phytomorphology 21:50–63Google Scholar
  3. Corriveau JL, Coleman AW (1988) Rapid screening method to detect potential biparental inheritance of plastid DNA and results for over 200 angiosperm species. Am J Bot 75:1443–1458Google Scholar
  4. Cruzan MB, Arnold ML, Carney SE, Wollenberg KR (1993) CpDNA inheritance in interspecific crosses and evolutionary inference in Louisiana irises. Am J Bot 80:344–350Google Scholar
  5. Dong J, Wagner DB, Yanchuk AD, Carlson MR, Magnussen S, Wang X-R, Szmidt AE (1992) Paternal chloroplast DNA inheritance in Pinus contorta and Pinus banksiana: independence of parental species or cross direction. J Hered 83:419–422Google Scholar
  6. Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 19:11–15Google Scholar
  7. Govindaraju DR, Wagner DB Smith GP, Dancik BP (1988) Chloroplast DNA variation within individual trees of a Pinus banksianaPinus contorta sympatric region. Can J For Res 18:1347–1350Google Scholar
  8. Lagercrantz U, Ellegren H, Andersson L (1993) The abundance of various polymorphic microsatellite motifs differs between plants and vertebrates. Nucleic Acids Res 21:1111–1115Google Scholar
  9. Lincoln SE, Daly MJ, Lander ES (1991) PRIMER Version 0.5: A computer program for automatically selecting PCR primers. Whitehead Institute for Biomedical Research, Cambridge, MAGoogle Scholar
  10. Moore SS, Sargeant LL, King TJ, Mattick JS, Georges M, Hetzel DJS (1991) The conservation of dinucleotide microsatellites among mammalian genomes allows the use of heterologous PCR primer pairs in closely related species. Genomics 10:654–660Google Scholar
  11. Moran GF, Bell JC, Eldridge KG (1988) The genetic structure and the conservation of the five natural populations of Pinus radiata. Can J For Res 18:506–514Google Scholar
  12. Morgante M, Olivieri AM (1993) PCR-amplified microsatellites as markers in plant genetics. Plant J 3:175–182Google Scholar
  13. Neale DB, Sederoff RR (1989) Paternal inheritance of chloroplast DNA and maternal inheritance of mitochondrial DNA in loblolly pine. Theor Appl Genet 77:212–216Google Scholar
  14. Neale DB, Wheeler NC, Allard RW (1986) Paternal inheritance of chloroplast DNA in Douglas-fir. Can J For Res 16:1152–1154Google Scholar
  15. Neale DB, Marshall KA, Sederoff RR (1989) Chloroplast and mitochondrial DNA are paternally inherited in Sequoia sempervirens D. Don Endl. Proc Natl Acad Sci USA 86:9347–9349Google Scholar
  16. Neale DB, Marshall KA, Harry DE (1991) Inheritance of chloroplast and mitochondrial DNA in incense-cedar (Calocedrus decurrens). Can J For Res 21:717–720Google Scholar
  17. Ohba K, Iwakawa M, Okada Y, Murai M (1971) Paternal transmission of a plastid anomaly in some reciprocal crosses of sugi, Cryptomeria japonica D. Don. Silvae Genet 20:101–107Google Scholar
  18. Owens JN, Morris SJ (1990) Cytological basis for cytoplasmic inheritance in Pseudotsuga menziesii. I. Pollen tube and archegonial development. Am J Bot 77:433–445Google Scholar
  19. Owens JN, Morris SJ (1991) Cytological basis for cytoplasmic inheritance in Pseudotsuga menziesii. II. Fertilization and proembroyo development. Am J Bot 78:1515–1527Google Scholar
  20. Powell W, Morgante M, McDevitt R, Vendramin GG, Rafalski AJ (1995) Polymorphic simple sequence repeat regions in chloroplast genomes: applications to the population genetics of pines. Proc Natl Acad Sci USA 92:7759–7763Google Scholar
  21. Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: a laboratory manual. 2nd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N. Y., pp 13.45–13.57Google Scholar
  22. Sears BB (1980) Elimination of plastids during spermatogenesis and fertilization in the plant kingdom (review). Plasmid 4:233–255Google Scholar
  23. Smith DN, Devey ME (1994) Occurrence and inheritance of microsatellites in Pinus radiata. Genomics 37:977–983Google Scholar
  24. Stine M, Keathley DE (1990) Paternal inheritance of plastids in Engelmann spruce x blue spruce hybrids. J Hered 81:443–446Google Scholar
  25. Stine M, Sears BB, Keathley DE (1989) Inheritance of plastids in interspecific hybrids of blue spruce and white spruce. Theor Appl Genet 78:768–774Google Scholar
  26. Szmidt AE, Aldèn T, Hällgren J-E (1987) Paternal inheritance of chloroplast DNA in Larix. Plant Mol Biol 9:59–64Google Scholar
  27. Szmidt AE, El-Kassaby YA, Sigurgeirsson A, Aldèn T, Lindgren D, Hällgren J-E (1988) Classifying seedlots of Picea sitchensis and P. glauca in zones of introgression using restriction analysis of chloroplast DNA. Theor Appl Genet 76:841–845Google Scholar
  28. Taberlet P, Gielly L, Pautou G, Bouvet J (1991) Universal primers for amplification of three non-coding regions of chloroplast DNA. Plant Mol Biol 17:1105–1109Google Scholar
  29. Tautz D (1989) Hypervariability of simple sequence as a general source for polymorphic DNA markers. Nucleic Acids Res 17:6463–6471Google Scholar
  30. Vicario F, Vendramin GG, Rossi P, Lio P, Giannini (1995) Allozyme, chloroplast DNA and RAPD markers for determining genetic relationships between Abies alba and the relic population of Abies nebrodensis. Theor Appl Genet 90:1012–1018Google Scholar
  31. Wakasugi T, Tsudzuki S, Ito S, Shibata M, Sugiura M (1994) A physical map and clone bank of the black pine (Pinus thunbergii) chloroplast genome. Plant Mol Biol Rep 12:227–241Google Scholar
  32. Wagner DB (1992) Nuclear, chloroplast, and mitochondrial DNA polymorphisms as biochemical markers in population genetic analyses of forest trees. New For 6:373–390Google Scholar
  33. Wagner DB, Furnier GR, Saghai-Maroof MA, Williams SM, Dancik BP, Allard RW (1987) Chloroplast DNA polymorphisms in lodgepole and jack pines and their hybrids. Proc Natl Acad Sci USA 84:2097–2100Google Scholar
  34. Wagner DB, Govindaraju DR, Yeatman CW, Pitel JA (1989) Paternal chloroplast DNA inheritance in a diallel cross of jack pine (Pinus banksiana Lamb.). J Hered 80:483–485Google Scholar
  35. Weir S (1990) Genetic data analysis. Sinauer Assoc, Sunderland, Mass.Google Scholar
  36. Whatley JM (1982) Ultrastructure of plastid inheritance: green algae to angiosperms. Bot Rev 57:527–569Google Scholar
  37. Wheeler NC, KS Jech (1992) The use of electrophoretic markers in seed orchard research. New For 6:311–328Google Scholar
  38. White EE (1990) Chloroplast DNA in Pinus monticola 2. Survey of within-species variability and detection of heteroplasmic individuals. Theor Appl Genet 79:251–255Google Scholar
  39. Wolf KH, Li H-H, Sharp PM (1987) Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs. Proc Natl Acad Sci USA 88:9054–9058Google Scholar

Copyright information

© Springer-Verlag 1996

Authors and Affiliations

  • S. A. Cato
    • 1
  • T. E. Richardson
    • 1
  1. 1.New Zealand Forest Research InstituteRotoruaNew Zealand

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