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

Open access

Abstract

Pinus kesiya (Khasi pine) is the principal pine species in northeast India having high commercial value. Chloroplast microsatellites (cpSSR) were used to study the genetic diversity and population genetic structure of 10 populations of P. kesiya covering entire natural range of distribution in India. A total of 33 primer pairs (cpSSRs) of P. thunberghii and P. sylvestris were tested in P. kesiya for their transferability, out of which 18 chlo­roplast primers showed positive amplification and 10 were found polymorphic. A total of 250 individuals from 10 different populations were genotyped using the selected 10 cpSSRs. When alleles at each of the 10 loci were jointly analysed a total of 36 size variants were discovered, which combined to desig­nate 90 haplotypes among 250 individuals. None of the haplo­type was found common among the populations as they were population specific. The cpSSR indicated that P. kesiya popula­tions have maintained a moderately high genetic diversity (HT=0.638) which is typical in most coniferous species. Howe­ver, the inter-population genetic diversity was higher than the intra population diversity and the genetic differentiation bet­ween populations was also found to be very high (FST=0.47). A Bayesian cluster analysis separated the populations into six clusters where most of the individuals were found in single population clusters with minor admixtures. The distribution of genetic diversity and sub structuring of P. kesiya reflect week pollen mediated gene flow due to geographic isolation and genetic drift. The study has revealed useful cpSSR markers for P. kesiya, which were lacking earlier and also added an insight into the state of Khasi pine forest in the region, which can be useful for the better management and future conservation programs.

If the inline PDF is not rendering correctly, you can download the PDF file here.

  • 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.x

  • AVISE JC (1994) Molecular Markers Natural History and Evolution. Chapman and Hall New York. https://doi.org/10.1007/978-1-4615-2381-9

  • 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.x

  • 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.1600126

  • 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.

  • CHAUHAN P (2011) Molecular genetic analysis of Chir pine (Pinus roxburghiiSar­gh.) through microsatellite markers. Ph.D. Thesis submitted to Forest Re­search Institute (Deemed) University.

  • 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 Resourc­es11: 219-222.

  • CLARK CM WENTWORTH TR O’MALLEY DM(2000) Genetic discontinuity re­vealed by chloroplastmicrosatellites in Eastern North AmericanAbies (Pina­ceae). American Journal of Botany87: 774-782. https://doi.org/10.2307/2656885

  • 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.x

  • CORANDER J WALDMANN P SILLANPAA MJ (2003) Bayesian analysis of genetic differentiation between populations. Genetics 163: 367-374.

  • CORANDER J WALDMANN P MARTTINEN P SILLANPAA MJ (2004) BAPS 2: en­hanced possibilities for the analysis of genetic population structure. Bioin­formatics20: 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.

  • 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/10.2307/2656576

  • 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/mcs044

  • 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.x

  • 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-z

  • ELLEGREN H (2004) Microsatellites: simple sequences with complex evolution. Nature Reviews Genetics 5: 435-445. https://doi.org/10.1038/nrg1348

  • 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/10.1177/117693430500100003

  • 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.

  • FRANKHAM R BRISCOE DA BALLOU JD (2002) Introduction to conservation ge­netics. Cambridge University Press New York New York USA. https://doi.org/10.1017/cbo9780511808999

  • 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-z

  • GΌMEZ A GONZÁLEZ- MARTÍNEZ SC COLLADA C CLIMENT J GIL L (2003) Com­plex population genetic structure in the endemic Canary Islandpine re­

  • vealed using chloroplast microsatellite markers. Theoretical and Applied Genetics 107:1123-1131. https://doi.org/10.1007/s00122-003-1320-2

  • 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.

  • 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-y

  • HARTL DL CLARK AG (1997) Principles of Population Genetics 3rdedn. Sinauer Associates Inc Sunderland MA.

  • 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

  • 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/10.2307/3558425

  • 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.v30.002

  • MCDERMOTT JM MCDONALD BA (1993) Gene flow in plant pathosystems. Annu. Rev. Phytopathol31: 353-373. https://doi.org/10.1146/annurev.py.31.090193.002033

  • 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)90039-2

  • 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/2011202-11449

  • 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/bf00266189

  • NEI M (1987) Molecular Evolutionary Genetics. Columbia University Press New York. https://doi.org/10.1016/0047-2484(89)90093-6

  • PERRY JP (1991) The Pines of Mexico and Central America. Timber Press Port­landOR. https://doi.org/10.2307/1222523

  • 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/d6020283

  • 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.1998.0491

  • 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)

  • 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 Ecology11: 869-877. https://doi.org/10.1046/j.1365-294x.2002.01490.x

  • 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.106.066613

  • 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.6882870

  • STANGE C PREHN D JOHNSON PA (1998) Isolation of Pinus radiata genomic DNA suitable for RAPD analysis. Plant Molecular Biology Reporter 16: 1-8.

  • 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.93.9.1274

  • 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.2005.1680

  • 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.x

  • 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/s001220050917

  • 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-43-1-68

  • 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 Research13: 7571-7576. https://doi.org/10.4238/2014.september.12.24

  • 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/cropsci2003.1828

  • 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/bf02344555

  • WRIGHT S (1951) The genetical structure of populations. Annals of Eugenics15: 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/bf02858189

  • 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 Re­source5(4):1113-1114. https://doi.org/10.1007/s12686-013-9964-y

  • 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
Journal information
Impact Factor

IMPACT FACTOR 2018: 0.741
5-year IMPACT FACTOR: 0.651

CiteScore 2018: 0.77

SCImago Journal Rank (SJR) 2018: 0.345
Source Normalized Impact per Paper (SNIP) 2018: 0.362

Cited By
Metrics
All Time Past Year Past 30 Days
Abstract Views 0 0 0
Full Text Views 267 153 1
PDF Downloads 228 140 5