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, 9:60 | Cite as

Genetic diversity and structure of Dendrocalamus hamiltonii natural metapopulation: a commercially important bamboo species of northeast Himalayas

  • Rajendra K. MeenaEmail author
  • Maneesh S. Bhandhari
  • Santan Barhwal
  • Harish S. Ginwal
Original Article
  • 7 Downloads

Abstract

Dendrocalamus hamiltonii is a commercially important bamboo species of India, experiencing population depletion due to heavy extraction from natural forests. Nuclear simple sequence repeats (nSSRs) were used to study the genetic diversity and population genetic structure of 19 natural stands of D. hamiltonii distributed across the northeast Himalayas. A total of 68 nSSR primer pairs of D. latiflorus and Bambusa arundinacea have been tested in D. hamiltonii for their transferability, out of which 17 primers showing positive and polymorphic amplification were used for genotyping. A total of 130 alleles were generated in 535 individuals of all the populations using selected primer pairs. The marker analysis indicated that D. hamiltonii populations have maintained a low level of genetic diversity (h = 0.175, I = 0.291) in northeastern region of India. Despite a large proportion of the genetic variation (83.47%) confined within the populations, a moderate level of genetic differentiation (FST = 0.165) was observed among the populations. The clustering pattern obtained in UPGMA and STRUCTURE analysis revealed that most of the populations were clustered in accordance with their geographical distribution. Two populations (DH03 and DH13) exhibiting significant genetic admixture were identified and recommended for in situ conservation. In addition, six highly diverse populations were also suggested for conservation in different geographical area under study. The study has revealed useful nSSR markers for D. hamiltonii, which were lacking earlier and the information generated herein is of paramount importance in devising programs for species conservation and genetic improvement.

Keywords

Bamboo Dendrocalamus hamiltonii Genetic diversity Genetic differentiation Genetic structure nSSR 

Notes

Acknowledgements

The authors are thankful to Science Engineering and Research Board (SERB), New Delhi, India, for providing financial support. The field and laboratory facilities provided by Directors (RFRI, Jorhat and FRI, Dehradun) for execution of work is also duly acknowledged. We are thankful to the forest departments of Mizoram, Assam, Nagaland, Meghalaya and Arunachal Pradesh for granting necessary permissions and providing support during sample collection.

Compliance with ethical standards

Conflict of interest

On behalf of all authors, the corresponding author states that there is no conflict of interest.

Supplementary material

13205_2019_1591_MOESM1_ESM.pdf (335 kb)
Supplementary material 1 (PDF 335 KB)

References

  1. Abreu AG, Grombone-Guaratini MT, Monteiro M, Pinheiro JB, Tombolato AFC, Zucchi MI (2011) Development of microsatellite markers for Aulonemia aristulata (Poaceae) and cross-amplification in other bamboo species. Am J Bot 98:90–92.  https://doi.org/10.3732/ajb.1000511 CrossRefGoogle Scholar
  2. Attigala L, Gallaher T, Nason J, Clark LG (2017) Genetic diversity and population structure of the threatened temperate woody bamboo Kuruna debilis (Poaceae: Bambusoideae: Arundinarieae) from Sri Lanka based on microsatellite analysis. J Natl Sci Found Sri 45(1):53–65.  https://doi.org/10.4038/jnsfsr.v45i1.8038 CrossRefGoogle Scholar
  3. Banik RL (2016) Silviculture of South Asian priority bamboos. Springer, Singapore.  https://doi.org/10.1007/978-981-10-0569-5 CrossRefGoogle Scholar
  4. Barkley NA, Newman ML, Wang ML, Hotchkiss MW, Pederson GA (2005) Assessment of the genetic diversity and phylogenetic relationships of a temperate bamboo collection by using transferred EST-SSR markers. Genome 48(4):731–737.  https://doi.org/10.1139/g05-022 CrossRefPubMedGoogle Scholar
  5. Ben-zhi Z, Mao-yi F, Jin-zhong X, Xiao-sheng Y, Zheng-cai L (2005) Ecological functions of bamboo forest: research and application. J For Res 16:143–147.  https://doi.org/10.1007/BF02857909 CrossRefGoogle Scholar
  6. Bhandawat A, Sharma V, Sharma H, Sood A, Sharma RK (2014) Development and crosstransferability of functionally relevant micro-satellite markers in Dendrocalamus latiflorus and related bamboo species. J Genet 93:e48–e55.  https://doi.org/10.1007/s12041-014-0377-9 CrossRefPubMedGoogle Scholar
  7. Chaluvaraju D, Singh BS, Nageswara Rao M, Ravikanth G, Ganeshaiah KN, Uma Shaanker R (2001) Conservation of bamboo genetic resources in Western Ghats: status, threats and strategies. In: Uma Shaanker R, Ganeshaiah KN, Bawa KS (eds) Forest genetic resources: status, threats and conservation strategies. Oxford-IBH Publication, New Delhi, pp 99–113Google Scholar
  8. De Vicente MC, Lopez C, Fulton T (2004) Genetic diversity analysis with molecular marker data: learning module, vol 2. IPGRI, Rome and Cornell University, New York. https://www.bioversityinternational.org/e-library/publications/detail/molecular-marker-learning-modulesvols-1-and-2/ Google Scholar
  9. Desai P, Gajera B, Mankad M et al (2015) Comparative assessment of genetic diversity among Indian bamboo genotypes using RAPD and ISSR markers. Mol Biol Rep 42(8):1265–1273.  https://doi.org/10.1007/s11033-015-3867-9 CrossRefPubMedGoogle Scholar
  10. Dong YR, Yang HQ (2014) Development of seventeen novel microsatellite markers of a wild and flowering bamboo Dendrocalamus membranaceus (Poaceae) and cross-amplification in Dendrocalamus genus. Conserv Genet Resour 6(1):201–203.  https://doi.org/10.1007/s12686-013-0055-x CrossRefGoogle Scholar
  11. Dong WJ, Wu MD, Lin Y, Zhou MB, Tang DQ (2011) Evaluation of 15 caespitose bamboo EST-SSR markers for cross-species/genera transferability and ability to identify interspecies hybrids. Plant Breed 130:596–600.  https://doi.org/10.1111/j.1439-0523.2011.01860.x CrossRefGoogle Scholar
  12. Dong Y, Zhang Z, Yang H (2012) Sixteen novel microsatellite markers developed for Dendrocalamus sinicus (Poaceae), the strongest woody bamboo in the world. Am J Bot 99(9):e347–e349.  https://doi.org/10.3732/ajb.1200029 CrossRefPubMedGoogle Scholar
  13. Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf material. Phytochem Bull 19:11–15Google Scholar
  14. Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14(8):2611–2620.  https://doi.org/10.1111/j.1365-294X.2005.02553.x CrossRefPubMedGoogle Scholar
  15. Excoffier L, Laval G, Schneider S (2005) Arlequin ver. 3.0: an integrated software package for population genetics data analysis. Evol Bioinform Online 1:47–50CrossRefGoogle Scholar
  16. Frankham R (2008) Genetic adaptation to captivity in species conservation programs. Mol Ecol 17(1):325–333.  https://doi.org/10.1111/j.1365-294X.2007.03399.x CrossRefPubMedGoogle Scholar
  17. FSI (2017) India state of forest report. Forest Survey of India, DehradunGoogle Scholar
  18. Garcia-Verdugo C, Calleja JA, Vargas P, Silva L, Moreira O, Pulido F (2013) Polyploidy and microsatellite variation in the relict tree Prunus lusitanica L.: how effective are refugia in preserving genotypic diversity of clonal taxa? Mol Ecol 22(6):1546–1557.  https://doi.org/10.1111/mec.12194 CrossRefPubMedGoogle Scholar
  19. George S, Sharma J, Yadon VL (2009) Genetic diversity of the endangered and narrow endemic Piperia yadonii (Orchidaceae) assessed with ISSR polymorphisms. Am J Bot 96(11):2022–2030.  https://doi.org/10.3732/ajb.0800368 CrossRefPubMedGoogle Scholar
  20. Gilpin ME, Soule ME (1986) Minimum viable populations: processes of species extinction. In: Soule ME (ed) Conservation biology: the science of scarcity and diversity. Sinauer, Sunderland, pp 19–34Google Scholar
  21. Greco TM, Pinto MM, Tombolato AFC, Xia N (2015) Diversity of bamboo in Brazil. J Trop Subtrop Bot 23(1):1–16.  https://doi.org/10.11926/j.issn.1005-3395.2015.01.001 CrossRefGoogle Scholar
  22. Hamrick JL, Godt MJW (1990) Allozyme diversity in plant species. In: Brown AHD, Clegg MT, Kahler AL, Weir BS (eds) Plant population genetics, breeding, and genetic resources. Sinauer Associates Inc., Sunderland, pp 43–63Google Scholar
  23. Hamrick JL, Godt MJW (1996) Effects of life history traits on genetic diversity in plant species. Philos Trans R Soc B 351:1291–1298.  https://doi.org/10.1098/rstb.1996.0112 CrossRefGoogle Scholar
  24. Janzen DH (1976) Why bamboos wait so long to flower. Annu Rev Ecol Syst 7:347–391.  https://doi.org/10.1146/annurev.es.07.110176.002023 CrossRefGoogle Scholar
  25. Kaneko S, Franklin DC, Yamasaki N, Isagi Y (2008) Development of microsatellite markers for Bambusa arnhemica (Poaceae: Bambuseae), a bamboo endemic to northern Australia. Conserv Genet 9(5):1311–1313.  https://doi.org/10.1007/s10592-007-9467-z CrossRefGoogle Scholar
  26. Kitamura K, Saitoh T, Matsuo A, Suyama Y (2009) Development of microsatellite markers for the dwarf bamboo species Sasa cernua and Sasa kurilensis (Poaceae) in northern Japan. Mol Ecol Resour 9(6):1470–1472.  https://doi.org/10.1111/j.1755-0998.2009.02675.x CrossRefPubMedGoogle Scholar
  27. Lande R (1988) Genetics and demography in biological conservation. Science 241(4872):1455–1460.  https://doi.org/10.1126/science.3420403 CrossRefPubMedGoogle Scholar
  28. Lin Y, Lu J, Wu MD, Zhou MB, Wei F, Ide Y, Tang D (2014) Identification, cross-taxon transferability and application of full-length cDNA SSR markers in Phyllostachys pubescens. Springer Plus 3:486.  https://doi.org/10.1186/2193-1801-3-486 CrossRefPubMedGoogle Scholar
  29. Ma QQ, Song HX, Zhou SQ, Yang WQ, Li DS, Chen JS (2013) Genetic structure in dwarf bamboo (Bashania fangiana) clonal populations with different genet ages. PLoS One 8(11):e78784.  https://doi.org/10.1371/journal.pone.0078784 CrossRefPubMedPubMedCentralGoogle Scholar
  30. Mantel N (1967) The detection of disease clustering and a generalized regression approach. Cancer Res 27:209–220PubMedGoogle Scholar
  31. Mason AS (2015) SSR genotyping. In: Batley J (ed) Plant genotyping. Springer, New York, pp 77–89Google Scholar
  32. Nag A, Gupta P, Sharma V, Sood A, Ahuja SP, Sharma KR (2013) AFLP and RAPD based genetic diversity assessment of industrially important reed bamboo (Ochlandra travancorica Benth). J Plant Biochem Biot 22:144–149.  https://doi.org/10.1007/s13562-012-0114-5 CrossRefGoogle Scholar
  33. Nageswara Rao M, Ganeshaiah KN, Uma Shaanker R (2007) Assessing threats and mapping sandal (Santalum album L.) resources in peninsular India: identification of genetic hot-spot for in-situ conservation. Conserv Genet 8:925–935.  https://doi.org/10.1007/s10592-006-9247-1 CrossRefGoogle Scholar
  34. Naithani HB (2008) Diversity of Indian bamboos with special reference to North-east India. Indian For 134(6):765–788Google Scholar
  35. Nayak S, Rout GR (2005) Isolation and characterization of microsatellites in Bambusa arundinacea and cross species amplification in other bamboos. Plant Breed 124(6):559–602.  https://doi.org/10.1111/j.1439-0523.2005.01102.x CrossRefGoogle Scholar
  36. Nayak S, Rout GR, Das P (2003) Evaluation of genetic variability in bamboo using RAPD markers. Plant Soil Environ 49:24–28CrossRefGoogle Scholar
  37. Ndiaye A, Rivallan R, Legavre T, Brunel D, Sagna M, Gassama YK, Risterucci AM (2013) Isolation, characterization and cross-species amplification of polymorphic microsatellite markers for Oxytenanthera abyssinica (A. Rich.) Munro (Poaceae). Conserv Genet Resour 5(3):799–802.  https://doi.org/10.1007/s12686-013-9911-y CrossRefGoogle Scholar
  38. Nei M (1972) Genetic distance between populations. Am Nat 106:283–292CrossRefGoogle Scholar
  39. Nilkanta H, Amom T, Tikendra L, Rahaman H, Nongdam P (2017) ISSR marker based population genetic study of Melocanna baccifera (Roxb.) Kurz: a commercially important bamboo of Manipur, North-East India. Scientifica 2017:1–9.  https://doi.org/10.1155/2017/3757238 CrossRefGoogle Scholar
  40. Nybom H, Bartish IV (2000) Effects of life history traits and sampling strategies on genetic diversity estimates obtained with RAPD markers in plants. Perspect Plant Ecol 3:293–114.  https://doi.org/10.1078/1433-8319-00006 CrossRefGoogle Scholar
  41. Obbard DJ, Harris SA, Pannell JR (2006) Simple allelic-phenotype diversity and differentiation statistics for allopolyploids. Heredity 97:296–303.  https://doi.org/10.1038/sj.hdy.6800862 CrossRefPubMedGoogle Scholar
  42. Ohrnberger D (1999) The bamboos of the world: annotated nomenclature and literature of the species and the higher and lower taxa. Elsevier, Amsterdam, p 526Google Scholar
  43. Peakall R, Smouse PE (2012) GenAlEx 6.5: genetic analysis in Excel. Population genetics software for teaching and research-an update. Bioinformatics 28(19):2537–2539.  https://doi.org/10.1093/bioinformatics/bts460 CrossRefPubMedPubMedCentralGoogle Scholar
  44. Peng Z, Lu Y, Li L, Zhao et al (2013) The draft genome of the fast-growing non-timber forest species moso bamboo (Phyllostachys heterocycla). Nat Genet 45(4):456–461.  https://doi.org/10.1038/ng.2569 CrossRefPubMedGoogle Scholar
  45. Pfeiffer T, Roschanski AM, Pannell JR, Korbecka G, Schnittler M (2011) Characterization of microsatellite loci and reliable genotyping in a polyploid plant, Mercurialis perennis (Euphorbiaceae). J Hered 102:479–488.  https://doi.org/10.1093/jhered/esr024 CrossRefPubMedGoogle Scholar
  46. 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 CrossRefGoogle Scholar
  47. Potter KM, Jetton RM, Bower A, Jacobs DF, Man G, Hipkins VD, Westwood M (2017) Banking on the future: progress, challenges and opportunities for the genetic conservation of forest trees. N For 48(2):153–180.  https://doi.org/10.1007/s11056-017-9582-8 CrossRefGoogle Scholar
  48. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155(2):945–959PubMedPubMedCentralGoogle Scholar
  49. Prober SM, Brown AHD (1994) Conservation of the grassy white box woodlands: Population genetics and fragmentation of Eucalyptus albens. Conserv Biol 8(4):1003–1013.  https://doi.org/10.1046/j.1523-1739.1994.08041003.x CrossRefGoogle Scholar
  50. Quattro JM, Vrijenhoek RC (1989) Fitness differences among remnant populations of the endangered Sonoran topminnow. Science 245:976–978. https://www.ncbi.nlm.nih.gov/pubmed/2772650
  51. Rai KC, Ginwal HS (2018) Microsatellite analysis to study genetic diversity in Khasi Pine (Pinus kesiya Royle Ex. Gordon) using chloroplast SSR markers. Silvae Genet 67:99–105.  https://doi.org/10.2478/sg-2018-0014 CrossRefGoogle Scholar
  52. Ramanatha Rao V, Hodgkin T (2002) Genetic diversity and conservation and utilization of plant genetic resources. Plant Cell Tissue Organ Cult 68:1–19.  https://doi.org/10.1023/A:1013359015812 CrossRefGoogle Scholar
  53. Ravikanth G, Nageswara Rao M, Singh D, Cheluvaraju J, Ganeshaiah KN, Uma Shaanker R (2008) Contrasting spatial patterns of distribution of genetic diversity in two important bamboo species in the Central Western Ghats, India. J Bamboo Rattan 7(1&2):41–52Google Scholar
  54. Salam K (2013) Connecting the poor: bamboo (problems and prospect). South Asia Bamboo Foundation (SABF). http://studylib.net/doc/6959674. Accessed 17 Dec 2017
  55. Salam K, Pongen Z (2008) Hand book on bamboo. Cane & Bamboo Technology Centre Guwahati, AssamGoogle Scholar
  56. Sampson JF, Byrne M (2012) Genetic diversity and multiple origins of polyploidy Atriplex nummularia Lindl. (Chenopodiaceae). Biol J Linn Soc 105:218–230.  https://doi.org/10.1111/j.1095-8312.2011.01787.x CrossRefGoogle Scholar
  57. Seethalakshmi KK (2001) Biodiversity, conservation and genetic improvement of bamboo. In: Uma Shaanker R, Ganeshaiah KN, Bawa KS (eds) Forest genetic resources: status, threats and conservation strategies. Oxford-IBH Publication, New Delhi, pp 225–235Google Scholar
  58. Seethalakshmi KK, Kumar M (1998) Bamboos of India—a compendium. Kerala Forest Research Institute, Peechi and International Network for Bamboo and Rattan, New DelhiGoogle Scholar
  59. Sharma ML, Nirmala C (2015) Bamboo diversity of India: an update. In: Proceedings of the 10th world bamboo congress, Damyang, Korea, 17–22 September 2015, pp 516–528Google Scholar
  60. Sharma V, Bhardwaj P, Kumar R, Sharma RK, Sood A, Ahuja PS (2009) Identification and cross-species amplification of EST derived SSR markers in different bamboo species. Conserv Genet 10(3):721–724.  https://doi.org/10.1007/s10592-008-9630-1 CrossRefGoogle Scholar
  61. Sood S, Walia S, Gupta M, Sood A (2013) Nutritional characterization of shoots and other edible products of an edible bamboo—Dendrocalamus hamiltonii. Curr Res Nutr Food Sci 1(2):169–176.  https://doi.org/10.12944/CRNFSJ.1.2.08 CrossRefGoogle Scholar
  62. Stapleton CM, Rao VR (1995) Progress and prospects in genetic diversity studies on bamboo and its conservation. Bamboo, people and the environment. In: Proceedings of international bamboo congress & workshop—4th WBC, Indonesia, June 19–22Google Scholar
  63. Teixeira H, Rodrıguez-Echeverrıa S, Nabais C (2014) Genetic diversity and differentiation of Juniperus thurifera in Spain and Morocco as determined by SSR. PLoS One 9(2):e88996.  https://doi.org/10.1371/journal.pone.0088996 CrossRefPubMedPubMedCentralGoogle Scholar
  64. Templeton AR, Routman E, Phillips CA (1995) Separating population structure from population history: a cladistic analysis of the geographical distribution of mitochondrial DNA haplotypes in the tiger salamander, Ambystoma tigrinum. Genetics 140(2):767–782PubMedPubMedCentralGoogle Scholar
  65. Thakur A, Barthwal S, Ginwal HS (2015) Genetic diversity in bamboos: conservation and improvement for productivity. In: Kaushik S, Singh YP, kumar D, Thapaliyal M, Barthwal S (eds) Bamboos in India. ENVIS Centre on Forestry, Dehradun, pp 131–146Google Scholar
  66. Tian B, Yang HQ, Wong KM, Liu AZ, Ruan ZY (2012) ISSR analysis shows low genetic diversity versus high genetic differentiation for giant bamboo, Dendrocalamus giganteus (Poaceae: Bambusoideae), in China populations. Genet Resour Crop Evol 59:901–908.  https://doi.org/10.1007/s10722-011-9732-3 CrossRefGoogle Scholar
  67. Tomar JMS, Hore HS, Annadurai A (2009) Bamboos and their conservation in northeast India. Indian For 135(6):817–824Google Scholar
  68. Triplett JK, Clark LG, Fisher AE, Wen J (2014) Independent allopolyploidization events preceded speciation in the temperate and tropical woody bamboos. N Phytol 204(1):66–73.  https://doi.org/10.1111/nph.12988 CrossRefGoogle Scholar
  69. Vorontsova MS, Clark LG, Dransfield J, Govaerts R, Wilkinson T, Baker WJ (2016) World atlas of bamboos and rattan. International Network of Bamboo and Rattan & Royal Botanic Gardens, KewGoogle Scholar
  70. Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evolution 38(6):1358–1370.  https://doi.org/10.2307/2408641 CrossRefPubMedGoogle Scholar
  71. Wright S (1978) Evolution and the genetics of populations: a treatise in four volumes. In: Variability within and among natural populations, vol 4. University of Chicago Press, ChicagoGoogle Scholar
  72. Yang HQ, An MY, Gu ZJ, Tian B (2012) Genetic diversity and differentiation of Dendrocalamus membranaceus (Poaceae: Bambusoideae), a declining bamboo species in Yunnan, China, as based on inter-simple sequence repeat (ISSR) analysis. Int J Mol Sci 13:4446–4457.  https://doi.org/10.3390/ijms13044446 CrossRefPubMedPubMedCentralGoogle Scholar
  73. Yeasmin L, Ali MN, Gantait S, Chakraborty S (2015) Bamboo: an overview on its genetic diversity and characterization. 3 Biotech 5(1):1–11.  https://doi.org/10.1007/s13205-014-0201-5 CrossRefPubMedGoogle Scholar
  74. Yeh FC, Yang RC, Boyles TBJ, Ye ZH, Mao JX (1999) POPGENE version 1.32: microsoft window-based freeware for population genetics analysis. Molecular Biology and Biotechnology Centre, University of Alberta, EdmontonGoogle Scholar

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© King Abdulaziz City for Science and Technology 2019

Authors and Affiliations

  1. 1.Division of Genetics and Tree ImprovementForest Research InstituteDehradunIndia

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