Have a personal or library account? Click to login
Microsatellite Analysis to Study Genetic Diversity in Khasi Pine (Pinus Kesiya Royle Ex. Gordon) Using Chloroplast SSR Markers Cover

Microsatellite Analysis to Study Genetic Diversity in Khasi Pine (Pinus Kesiya Royle Ex. Gordon) Using Chloroplast SSR Markers

Silvae Genetica
Volume 67 (2018): Issue 1 (February 2018)
By: Kirti Chamling Rai and  H. S. Ginwal  
Open Access
|Oct 2018

References

  1. AITKEN SN, YEAMAN S, HOLLIDAY JA, WANG T, CURTIS MCLANE S (2008) Adapta­tion, migration or extirpation: climate change outcomes for tree popula­tions. Evolutionary Applications, 1(1): 95-111. https://doi.org/10.1111/j.1752-4571.2007.00013.x10.1111/j.1752-4571.2007.00013.x
    Open DOISearch in Google ScholarBack to article
  2. AVISE JC (1994) Molecular Markers, Natural History and Evolution. Chapman and Hall, New York. https://doi.org/10.1007/978-1-4615-2381-910.1007/978-1-4615-2381-9
    Open DOISearch in Google ScholarBack to article
  3. BAYER C, FAY MF, DE BRUIJN AY, SAVOLAINEN V, MORTON CM, KUBITZKI K, AL­VERSON WS, CHASE MW (1999) Support for an expanded family concept of Malvaceae within recircumscribed order Malvales: a combined analysis of plastid atpB and rbcL DNA sequences. Botanical Journal of the Linnean So­ciety, 129: 267-303. https://doi.org/10.1111/j.1095-8339.1999.tb00505.x10.1111/j.1095-8339.1999.tb00505.x
    Open DOISearch in Google ScholarBack to article
  4. CAI N, XU Y, WANG D, CHEN S, LI G (2017) Identification and characterization of microsatellite markers in Pinus kesiya var. langbianensis (Pinaceae). Applica­tions in Plant Sciences, 5(2): 1-4. https://doi.org/10.3732/apps.160012610.3732/apps.1600126
    Open DOISearch in Google ScholarBack to article
  5. CATO SA, RICHARDSON TE (1996) Inter- and intraspecific polymorphism at chlo­roplast SSR loci and the inheritance of plastids in Pinus radiata D. Don. The­oretical and Applied Genetics, 93: 587-592. https://doi.org/10.1007/s001220050319 CHAUDHARY V, BHATTACHARYYA A (2002) Suitability of Pinus kesiya in Shillong, Meghalaya for tree-ring analysis, Current Science, 83(8): 1010-1015.10.1007/s001220050319CHAUDHARY(2002)PinuskesiyaMeghalayatree-83(8):1010-1015
    Open DOISearch in Google ScholarBack to article
  6. CHAUHAN P (2011) Molecular genetic analysis of Chir pine (Pinus roxburghiiSar­gh.) through microsatellite markers. Ph.D. Thesis submitted to Forest Re­search Institute (Deemed) University.
    Search in Google ScholarBack to article
  7. CHAUHAN P, GINWAL HS, RAWAT A, BARTHWAL S (2010) Cross-species amplifica­tion and characterization of chloroplast and nuclear microsatellite markers in Himalayan Chir Pine (Pinus roxburghii Sarg).Molecular Ecology Resourc­es,11: 219-222.
    Search in Google ScholarBack to article
  8. CLARK CM, WENTWORTH TR, O’MALLEY DM(2000) Genetic discontinuity re­vealed by chloroplastmicrosatellites in Eastern North AmericanAbies (Pina­ceae). American Journal of Botany,87: 774-782. https://doi.org/10.2307/265688510.2307/2656885
    Open DOISearch in Google ScholarBack to article
  9. CORANDER J, MARTTINEN P (2006) Bayesian identification of admixture events using multilocus molecular markers. Molecular Ecology, 15: 2833-2843. https://doi.org/10.1111/j.1365-294x.2006.02994.x10.1111/j.1365-294x.2006.02994.x
    Open DOISearch in Google ScholarBack to article
  10. CORANDER J, WALDMANN P, SILLANPAA MJ (2003) Bayesian analysis of genetic differentiation between populations. Genetics, 163: 367-374.10.1093/genetics/163.1.367
    Search in Google ScholarBack to article
  11. CORANDER J, WALDMANN P, MARTTINEN P, SILLANPAA MJ (2004) BAPS 2: en­hanced possibilities for the analysis of genetic population structure. Bioin­formatics,20: 2363-2369. https://doi.org/10.1093/bioinformatics/bth250 Bayesian analysis of population structure manual v. 6.0. http://www.helsinki.fi/bsg/software/BAPS/ Assessed 9 August 2018.10.1093/bioinformatics/bth250
    Search in Google ScholarBack to article
  12. DELGADO P, PINERO D, CHAOS A, PEREZ-NASSER N, ALVAREZ-BUYLLA ER (1999) High population differentiation and genetic variation in the endangered Mexican pine Pinus rzedowskii (Pinaceae). American Journal of Botany, 86(5): 669-676. https://doi.org/10.2307/265657610.2307/2656576
    Open DOISearch in Google ScholarBack to article
  13. DIEKMANN K, HODKINSON TR, BARTH S (2012) New chloroplast microsatellite markers suitable for assessing genetic diversity of Lolium perenne and oth­er related grass species. Annals of Botany, 110: 1327-1339. https://doi.org/10.1093/aob/mcs04410.1093/aob/mcs044347804222419761
    Open DOISearch in Google ScholarBack to article
  14. DOYLE JJ, DOYLE JL (1990) A rapid total DNA preparation procedure for fresh plant tissue. Focus, 12: 13-15. ECHT CS, DEVERNO LL, ANZIDEI M, VENDRAMIN GG (1998) Chloroplast microsat­ellite reveals population genetic diversity in red pine, Pinus resinosa Ait. Molecular Ecology, 7: 307-316. https://doi.org/10.1046/j.1365-294x.1998.00350.x10.1046/j.1365-294x.1998.00350.x
    Open DOISearch in Google ScholarBack to article
  15. ELIADES N-GH, GAILING O, LEINEMANN L, FADY B, FINKELDEY R (2011) High ge­netic diversity and significant population structure in Cedrus brevifolia Henry, a narrow endemic Mediterranean tree from Cyprus. Plant Systemat­ics and Evolution, 294: 185-198. https://doi.org/10.1007/s00606-011-0453-z10.1007/s00606-011-0453-z
    Open DOISearch in Google ScholarBack to article
  16. ELLEGREN H (2004) Microsatellites: simple sequences with complex evolution. Nature Reviews Genetics, 5: 435-445. https://doi.org/10.1038/nrg134810.1038/nrg134815153996
    Open DOISearch in Google ScholarBack to article
  17. EXCOFFIER L, LAVAL G, SCHNEIDER S (2005) Arlequin ver. 3.0: An integrated soft­ware package for population genetics data analysis. Evolutionary Bioinfor­matics Online, 1: 47-50. https://doi.org/10.1177/11769343050010000310.1177/117693430500100003
    Search in Google ScholarBack to article
  18. FALK DA, RICHARDS CM, MONTALVO AM; KNAPP EE (2006) Chapter 2: Popula­tion and ecological genetics in restoration ecology. In Foundations of resto­ration ecology. Edited by D.A. Falk, M.A. Palmer, and J.B. Zedler. Island Press, Washington, D. C. pp. 14-44.
    Search in Google ScholarBack to article
  19. FRANKHAM R, BRISCOE DA, BALLOU JD (2002) Introduction to conservation ge­netics. Cambridge University Press, New York, New York, USA. https://doi.org/10.1017/cbo978051180899910.1017/cbo9780511808999
    Open DOISearch in Google ScholarBack to article
  20. GANEA S, RANADE SS, HALL D, ABRAHAMSSON S, GARCIA-GIL MR (2015) Devel­opment and transferability of two multiplex nSSR in Scots pine (Pinus syl­vestris L.). Journal of Forestry Research, 26(2): 361-368. https://doi.org/10.1007/s11676-015-0042-z10.1007/s11676-015-0042-z
    Open DOISearch in Google ScholarBack to article
  21. GΌMEZ A, GONZÁLEZ- MARTÍNEZ SC, COLLADA C, CLIMENT J, GIL L (2003) Com­plex population genetic structure in the endemic Canary Islandpine re­
    Search in Google ScholarBack to article
  22. vealed using chloroplast microsatellite markers. Theoretical and Applied Genetics, 107:1123-1131. https://doi.org/10.1007/s00122-003-1320-210.1007/s00122-003-1320-214523525
    Open DOISearch in Google ScholarBack to article
  23. GΌMEZ- GARAY A, MASSELLI S, BUENO MA (2010) Distribution of Genetic Diver­sity of Pinus ayacahuite (Ehrenberg) at the Communal Forest of Totonica­pan, Guatemala. Bioremediation, Biodiversity and Bioavailability, 4: 35-41.
    Search in Google ScholarBack to article
  24. HAMRICK JL, GODT MJW (1992) Sherman-Broyles, S.L. Factors influencing levels of genetic diversity in woody plant species. New Forest, 6: 95-124. HANSEN OK, KJÆR ED, Vendramin GG (2005) Chloroplast microsatellite variation in Abies nordmanniana and simulation of causes for low differentiation among populations. Tree Genetics & Genomes, 1: 116-123. https://doi.org/10.1007/s11295-005-0016-y10.1007/s11295-005-0016-y
    Open DOISearch in Google ScholarBack to article
  25. HARTL DL, CLARK AG (1997) Principles of Population Genetics, 3rdedn. Sinauer Associates, Inc, Sunderland, MA.
    Search in Google ScholarBack to article
  26. KELCHNER SA (2000) The evolution of non-coding chloroplast DNA and its ap­plication in plant systematics. Annals of Missouri Botanical Garden, 87:499- 527. https://doi.org/10.2307/2666142 LEDIG FT, CAPΌ- ARTEAGA MA,10.2307/2666142FTCAPΌ-
    Open DOISearch in Google ScholarBack to article
  27. HODGSKISS PD, SBAY H, FLORES-LΌPEZ C, CON­KLE MT, BERMEJO-VELÁZQUEZ B (2001) Genetic diversity and the mating system of a rare Mexican Piñon, Pinus pinceana, and a comparison with Pi­nus maximartinezii (Pinaceae). American Journal of Botany, 88(11): 1977- 1987. https://doi.org/10.2307/355842510.2307/3558425
    Open DOISearch in Google ScholarBack to article
  28. LΌPEZ- VINYALLONGA S, LΌPEZ- ALVARADO J, CONSTANTINIDIS TH, SUSANNA A, GARCIA- JACAS N (2011) Microsatellite cross- species amplification in the genus Centaurea (Compositae), Collectanea Botanica, 30: 17-27. https://doi.org/10.3989/collectbot.2011.v30.00210.3989/collectbot.2011.v30.002
    Open DOISearch in Google ScholarBack to article
  29. MCDERMOTT JM, MCDONALD BA (1993) Gene flow in plant pathosystems. Annu. Rev. Phytopathol,31: 353-373. https://doi.org/10.1146/annurev.py.31.090193.00203310.1146/annurev.py.31.090193.002033
    Open DOISearch in Google ScholarBack to article
  30. MILLER CN (1982) Current status of Paleozoic and Mesozoic confers. Review of Palaeobotany and Palynology, 37: 99-114 (Cited by Millar, 1999) https://doi.org/10.1016/0034-6667(82)90039-210.1016/0034-6667(82)90039-2
    Open DOISearch in Google ScholarBack to article
  31. MIROV NT (1967) The genus Pinus. Ronald Press, New York, 602 pp. https://doi.org/10.2307/4004229 MORENO AC, MARCHELLI P, VENDRAMIN GG, GALLO LA (2011) Cross transfer­ability of SSRs to five species of Araucariaceae: useful tool for population genetic studies in Araucaria araucana. Forest Systems, 20(2): 303-314. https://doi.org/10.5424/fs/2011202-1144910.5424/fs/2011202-11449
    Search in Google ScholarBack to article
  32. MORGANTE M, PFEIFFER A, COSTACURTA A, OLIVIERI AM (1996) Molecular tools for population and ecological genetics in coniferous trees. Phyton-Annales Rei Botanicae, 36: 129- 138. NEALE DB, SEDEROFF RR (1989) Paternal inheritance of chloroplast DNA and maternal inheritance of mitochondrial DNA in loblolly pine. Theoretical and Applied Genetics, 77: 212-216. https://doi.org/10.1007/bf0026618910.1007/bf00266189
    Open DOISearch in Google ScholarBack to article
  33. NEI M (1987) Molecular Evolutionary Genetics. Columbia University Press, New York. https://doi.org/10.1016/0047-2484(89)90093-610.1016/0047-2484(89)90093-6
    Open DOISearch in Google ScholarBack to article
  34. PERRY JP (1991) The Pines of Mexico and Central America. Timber Press, Port­land,OR. https://doi.org/10.2307/122252310.2307/1222523
    Open DOISearch in Google ScholarBack to article
  35. PORTH I, EL-KASSABY YA (2014) Assessment of the genetic diversity in forest tree populations using molecular markers. Diversity, 6: 283-295. https://doi.org/10.3390/d602028310.3390/d6020283
    Open DOISearch in Google ScholarBack to article
  36. PROVAN J, SORANZO N, WILSON NJ, MCNICOL JW, FORREST GI, COTRELL J, POW­ELL E (1998) Genepool variation in Caledonia and European Scots pine (Pi­nus sylvestris L.) revealed by chloroplast Simple Sequence Repeats. In: Pro­ceedings of Royal Society of London, Series B, 265: 1697-1705. https://doi.org/10.1098/rspb.1998.049110.1098/rspb.1998.049116893569787466
    Open DOISearch in Google ScholarBack to article
  37. PROVAN J, SORANZO N, WILSON NJ, GOLDSTEIN DB, POWELL W (1999).A low mutation rate for chloroplast microsatellites. Genetics, 153: 943-947. QUELLER D, STRASSMANN J, HUGHES CR (1993)10.1093/genetics/153.2.943146078110511569
    Search in Google ScholarBack to article
  38. Microsatellites and kinship. Trends in Ecology and Evolution, 8:285-288. https://doi.org/10.1016/0169-5347(93)90256-o RIBEIRO MM, MARIETTE S, VENDRAMIN GG, SZMIDT AE, PLOMION C, KREMER A (2002) Comparison of genetic diversity estimates within and among popu­lations of maritime pine using chloroplast simple-sequence repeat and am­plified fragment length polymorphism data. Molecular Ecology,11: 869-877. https://doi.org/10.1046/j.1365-294x.2002.01490.x10.1046/j.1365-294X.2002.01490.x11975703
    Search in Google ScholarBack to article
  39. SCHUG MD, SMITH SG, TOZIER-PEARCEA, MCEVEY SF (2007):The genetic struc­ture of Drosophila ananassae populations from Asia, Australia and Samoa. Genetics, 175: 1429-1440. https://doi.org/10.1534/genetics.106.06661310.1534/genetics.106.066613184009117237518
    Open DOISearch in Google ScholarBack to article
  40. SINCLAIR WT, MONCUR JD, ENNOS RA (1997) Multiple origins for Scots pine (Pi­nus sylvestris L.) in Scotland: evidence from mitochondria DNA variation. Heredity, 80: 233-240. https://doi.org/10.1038/sj.hdy.688287010.1038/sj.hdy.6882870
    Open DOISearch in Google ScholarBack to article
  41. STANGE C, PREHN D, JOHNSON PA (1998) Isolation of Pinus radiata genomic DNA suitable for RAPD analysis. Plant Molecular Biology Reporter, 16: 1-8.10.1023/A:1007540901981
    Search in Google ScholarBack to article
  42. TERRAB A, PAUN O, TALAVERA S, TREMETSBERGER K, ARISTA M, STUESSY TF (2006) Genetic diversity and population structure in naturalpopulations of Moroccan Atlas Cedar (Cedrus atlantica; Pinaceae) determined with cpSSR markers. American Journal of Botany, 93: 1274-1280. https://doi.org/10.3732/ajb.93.9.127410.3732/ajb.93.9.127421642191
    Open DOISearch in Google ScholarBack to article
  43. TORO MA, CABALLERO A (2005) Characterization and conservation of genetic diversity in subdivided populations. Philosophical Transactions of the Royal Society, 360: 1367-1378. https://doi.org/10.1098/rstb.2005.168010.1098/rstb.2005.1680156950816048780
    Open DOISearch in Google ScholarBack to article
  44. VENDRAMIN GG, LELLILR ROSSI P, MORGANTE M (1996) A set of primers for the amplification of 20 chloroplast microsatellites in Pinaceae. Molecular Ecolo­gy, 5: 595-598. https://doi.org/10.1111/j.1365-294x.1996.tb00353.x10.1111/j.1365-294x.1996.tb00353.x8794566
    Open DOISearch in Google ScholarBack to article
  45. VENDRAMIN GG, ANZIDEI M, MADAGHIELE A, BUCCI G (1998) Distribution of ge­netic diversity in Pinus pinaster Ait. as revealed by chloroplast microsatel­lites. Theoretical and Applied Genetic, 97: 456- 463. https://doi.org/10.1007/s00122005091710.1007/s001220050917
    Open DOISearch in Google ScholarBack to article
  46. VENDRAMIN GG, ANZIDEI M, MADAGHIELE A, SPERISEN C, BUCCI G (2000) Chlo­roplast microsatellite analysis reveals the presence of population subdivi­sion in Norway spruce (Picea abies K.). Genome, 43: 68-78. https://doi.org/10.1139/gen-43-1-6810.1139/gen-43-1-68
    Open DOISearch in Google ScholarBack to article
  47. VILLALOBOS- ARÁMBULA AR, PÉRÉZ DE LA ROSA JA, ARIAS A, RAJORA OP (2014) Cross-species transferability of eastern white pine (Pinus strobus) nuclear microsatellite markers to five Mexican white pines. Genetics and Molecular Research,13: 7571-7576. https://doi.org/10.4238/2014.september.12.2410.4238/2014.september.12.24
    Open DOISearch in Google ScholarBack to article
  48. WANG D, SHI J, CARLSON SR, CREGAN PB, WARD RW, Diers BW (2003) Alow cost, high throughput Polyacrylamide gel electrophoresis system forgenotying with microsatellite DNA markers. Crop Science, 43: 1828-1832. https://doi.org/10.2135/cropsci2003.182810.2135/cropsci2003.1828
    Open DOISearch in Google ScholarBack to article
  49. WATANO Y, IMAZU M, SHIMIZU T (1996) Spatial distribution of cpDNA and mtD­NA haplotypes in a hybrid zone between Pinus pumila and P. parviflora var. pentaphylla. 2ndedn. Taylor &Francis Group, CRS Press, New York. https://doi.org/10.1007/bf0234455510.1007/bf02344555
    Open DOISearch in Google ScholarBack to article
  50. WRIGHT S (1951) The genetical structure of populations. Annals of Eugenics,15: 323-354. https://doi.org/10.1111/j.1469-1809.1949.tb02451.x XIANG-XIANG F, JI-SEN S (2005) Identification of seeds of Pinus species by Micro­satellite Markers. Journal of Forestry Research, 16(4): 281-284. https://doi.org/10.1007/bf0285818910.1007/BF02858189
    Search in Google ScholarBack to article
  51. XU Y, ZHANG R, TIAN B, BAI Q, WANG D, CAI N, HE C, KANG X, DUAN A (2013) De­velopment of novel microsatellite markers for Pinus yunnanensis and their cross amplification in congeneric species. Conservation Genetic Re­source,5(4):1113-1114. https://doi.org/10.1007/s12686-013-9964-y10.1007/s12686-013-9964-y
    Open DOISearch in Google ScholarBack to article
  52. YEH FC, YANG RC, BOYLE TBJ (1999) PopGene Version 1.31: Microsoft windows based Freeware for Population Genetic Analysis. University of Albert, Ed­monton. http://www.ualbert.ca/fyeh.
    Search in Google ScholarBack to article
DOI: https://doi.org/10.2478/sg-2018-0014 | Journal eISSN: 2509-8934 | Journal ISSN: 0037-5349
Journal RSS Feed
Language: English
Page range: 99 - 105
Published on: Oct 18, 2018
Published by: Johann Heinrich von Thünen Institute
In partnership with: Paradigm Publishing Services
Publication frequency: 1 issue per year
Keywords:
Simple sequence repeats,
cpSSR,
genetic diversity,
Khasi Pine,
P. kesiya
Related subjects:
Life sciences,
Molecular biology,
Genetics,
Biotechnology,
Plant science

© 2018 Kirti Chamling Rai, H. S. Ginwal, published by Johann Heinrich von Thünen Institute
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License.

Previous articleVolume 67 (2018): Issue 1 (February 2018)Next article