Advertisement

Agroforestry Systems

, Volume 88, Issue 5, pp 823–834 | Cite as

Genetic diversity analysis of switchgrass (Panicum virgatum L.) populations using microsatellites and chloroplast sequences

  • Madhugiri Nageswara-Rao
  • Micaha Hanson
  • Sujata Agarwal
  • C. Neal StewartJr.
  • Charles Kwit
Article

Abstract

The agricultural landscape of the United States could soon be changed by planting of switchgrass (Panicum virgatum L.) cultivars to meet government-mandated targets for lignocellulosic bioenergy production and consumption. This alteration could affect the genetic structure of wild switchgrass populations, which are native to the eastern half of North America through cultivar introgression. In this study, PCR amplification of microsatellite fragments as well as chloroplast gene-specific markers were utilized to quantify the genetic diversity and structure of five native populations and three agronomic fields (hereafter ‘populations’) planted with switchgrass cultivars. Microsatellite polymorphism across all the switchgrass populations ranged from 91.4 to 100 %. Overall, natural switchgrass populations had significantly higher mean genetic diversity than agronomic switchgrass cultivars (0.262 ± 0.102 and 0.201 ± 0.082 respectively, t test p < 0.008). Natural switchgrass populations had significantly higher total genetic diversity within (HS) and among (HT) as compared to agronomic switchgrass cultivars. A clear separation of natural and agronomic switchgrass populations was noted using principal component analysis and STRUCTURE analysis. A grouping pattern similar to that obtained in the microsatellite study was observed when chloroplast nucleotide sequence variation was assessed. In the realm of bioenergy sustainability, our results highlight the need to consider the genetic structure of cultivars for bioenergy when they are grown in proximity to native switchgrass populations.

Keywords

Agronomic cultivars Biofuel Chloroplast nucleotide sequencing Conservation and restoration Genetic variability Natural populations 

Notes

Acknowledgments

We thank numerous people who facilitated and assisted with field work, including B. Black, S. Bobzin, T. Crabtree, S. Jackson. We also thank G. Wein, X. Yang, D. Hadziabdic, R. Govindarajulu and P. A. Wadl for their assistance with laboratory and logistical assistance. Permits to collect switchgrass tissue from Tennessee State Natural Areas were obtained through the Tennessee Department of Environment and Conservation. This project was supported by Biotechnology Risk Assessment Grant Program competitive Grant No. 2010-39211-21699 from the USDA National Institute of Food and Agriculture (NIFA) as well as by Building Research Interest and Developing Global Engagement (BRIDGE), an Inter-College Undergraduate Research Funding Opportunity, awarded to M. Hanson. Neal Stewart Jr. also received support from the BioEnergy Science Center, a Bioenergy Research Center, supported by the Office of Biological and Environmental Research in the US Department of Energy Office of Science and funding from NIFA to the University of Tennessee Integrated Biomass Supply Systems (IBSS) Center.

Supplementary material

10457_2014_9728_MOESM1_ESM.doc (580 kb)
Supplementary material 1 (DOC 580 kb)

References

  1. Barnett FL, Carver RF (1967) Meiosis and pollen stainability in switchgrass, Panicum virgatum L. Crop Sci 7:301–304CrossRefGoogle Scholar
  2. Boshier DH, Chase MR, Bawa KS (1995) Population genetics of Cordia alliodora (Boraginaceae), a neotropical tree. 3. Gene flow, neighborhood, and population structure. Am J Bot 82:484–490CrossRefGoogle Scholar
  3. Burton G (1942) A cytological study of some species in the tribe Paniceae. Am J Bot 29:355–359CrossRefGoogle Scholar
  4. Casler MD, Stendal CA, Kapich L, Vogel KP (2007) Genetic diversity, plant adaptation regions, and gene pools for switchgrass. Crop Sci 47:2261–2273CrossRefGoogle Scholar
  5. Church GL (1940) Cytotaxonomic studies in the gramineae Spartina, Andropogon, and Panicum. Am J Bot 27:267–271CrossRefGoogle Scholar
  6. Clauss MJ, Cobban H, Mitchell-Olds T (2002) Cross-species microsatellite markers for elucidating population genetic structure in Arabidopsis and Arabis (Brassicaeae). Mol Ecol 11:591–601PubMedCrossRefGoogle Scholar
  7. Cortese LM, Honig J, Miller C, Bonos SA (2010) Genetic diversity of twelve switchgrass populations using molecular and morphological markers. Bioenergy Res 3:262–271CrossRefGoogle Scholar
  8. Costich DE, Friebe B, Sheehan MJ, Casler MD, Buckler ES (2010) Genome-size variation in switchgrass (Panicum virgatum): flow cytometry and cytology reveal rampant aneuploidy. Plant Genome 3:130–141CrossRefGoogle Scholar
  9. Delaney JT, Baack EJ (2012) Intraspecific chromosome number variation and prairie restoration—a case study in Northeast Iowa, U.S.A. Restor Ecol 20:576–583CrossRefGoogle Scholar
  10. Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software structure: a simulation study. Mol Ecol 14:2611–2620PubMedCrossRefGoogle Scholar
  11. Gascon C, Williamson GB, da Fonseca GAB (2000) Receding forest edges and vanishing reserves. Science 288:1356–1358PubMedCrossRefGoogle Scholar
  12. Gunter LE, Tuskan GA, Wullschleger SD (1996) Diversity among populations of switchgrass based on RAPD markers. Crop Sci 36:1017–1022CrossRefGoogle Scholar
  13. Hadziabdic D, Fitzpatrick BM, Wang X, Wadl PA, Rinehart TA, Ownley BH, Windham MT, Trigiano RN (2010) Analysis of genetic diversity in flowering dogwood natural stands using microsatellites: the effects of dogwood anthracnose. Genetica 138:1047–1057PubMedCrossRefGoogle Scholar
  14. Hamrick JL, Godt MJW (1989) Allozyme diversity in plant species. In: Brown AHD, Clegg MT, Kahler AL, Weir BS (eds) Plant population genetics, breeding and genetic resources. Sinauer Associates, Sunderland, pp 43–63Google Scholar
  15. Hamrick JL, Schnabel A (1985) Understanding the genetic structure of plant populations: some old problems and new approaches. In: Gregorius HR (ed) Population genetics in forestry. Springer, Berlin, pp 50–70CrossRefGoogle Scholar
  16. Honnay O, Jacquemyn H, Bossuyt B, Hermy M (2005) Forest fragmentation effects on patch occupancy and population viability of herbaceous plant species. New Phytol 166:723–736PubMedCrossRefGoogle Scholar
  17. Hopkins AA, Taliaferro CM, Murphy CD, Christian D (1996) Chromosome number and nuclear DNA content of several switchgrass populations. Crop Sci 36:1192–1195CrossRefGoogle Scholar
  18. Hu T, Li H, Li D, Sun J, Fu J (2011) Assessing genetic diversity of perennial ryegrass (Lolium perenne L.) from four continents by inter simple sequence repeat (ISSR) markers. Afr J Biotechnol 10:19365–19374Google Scholar
  19. Huang L-K, Bughrara SS, Zhang X-Q, Bales-Arcelo CJ, Bin X (2011) Genetic diversity of switchgrass and its relative species in Panicum genus using molecular markers. Biochem Syst Ecol 39:685–693CrossRefGoogle Scholar
  20. Hultquist SJ, Vogel KP, Lee DJ, Arumuganathan K, Kaeppler S (1996) Chloroplast DNA and nuclear DNA content variations among cultivars of switchgrass, Panicum virgatum L. Crop Sci 36:1049–1052CrossRefGoogle Scholar
  21. Kausch AP, Hague J, Oliver M, Li Y, Daniell H, Maschia P, Watrud LS, Stewart CN Jr (2010) Transgenic biofuel feedstocks and strategies for bioconfinement. Biofuels 1:163–176CrossRefGoogle Scholar
  22. Kwit C, Stewart CN Jr (2012) Gene flow matters in switchgrass (Panicum virgatum L.), a potential widespread biofuel feedstock. Ecol Appl 22:3–7PubMedCrossRefGoogle Scholar
  23. Kwit C, Moon HS, Warwick SI, Stewart CN Jr (2011) Transgene introgression in crop relatives: molecular evidence and mitigation strategies. Trends Biotechnol 29:284–293PubMedCrossRefGoogle Scholar
  24. Kwit C, Nageswara-Rao M, Stewart CN Jr (2014) Switchgrass: concerns, compliance and future prospects. In: Hong L, Wu Y (eds) Compendium of bioenergy plants: switchgrass. CRC Press, Taylor and Francis Group, Florida, pp 403–421Google Scholar
  25. Lannér C, Bryngelsson T, Gustafsson M (1997) Relationships of wild Brassica species with chromosome number 2n = 18, based on RFLP studies. Genome 40:302–308PubMedCrossRefGoogle Scholar
  26. Laurance WF (2000) Do edge effects occur over large spatial scales? Trends Ecol Evol 15:134–135PubMedCrossRefGoogle Scholar
  27. Lewis E (2013) The rate and characterization of hybridization between wild-type and cultivated switchgrass (Panicum virgatum L.) for biofuel use. A senior honors dissertation, The Ohio State UniversityGoogle Scholar
  28. Martinez-Reyna JM, Vogel KP (2002) Incompatibility systems in switchgrass. Crop Sci 42:1800–1805CrossRefGoogle Scholar
  29. McDonald RI, Fargione J, Kiesecker J, Miller WM, Powell J (2009) Energy sprawl or energy efficiency: climate policy impacts on natural habitat for the United States of America. PLoS One 4:e6802. doi: 10.1371/journal.pone.0006802 PubMedCentralPubMedCrossRefGoogle Scholar
  30. McLaughlin SB, Kszos LA (2005) Development of switchgrass (Panicum virgatum) as a bioenergy feedstock in the United States. Biomass Bioenergy 28:515–535CrossRefGoogle Scholar
  31. Missaoui AM, Paterson AH, Bouton JH (2006) Molecular markers for the classification of switchgrass (Panicum virgatum L.) germplasm and to assess genetic diversity in three synthetic switchgrass populations. Genet Resour Crop Evol 53:1291–1302CrossRefGoogle Scholar
  32. Monestiez P, Goulard M, Charmet G (1994) Geostatistics for spatial genetic structures: study of wild populations of perennial ryegrass. Theor Appl Genet 88:33–41PubMedCrossRefGoogle Scholar
  33. Morgante M, Olivieri AM (1993) PCR-amplified microsatellite as markers in plant genetics. Plant J 3:175–182PubMedCrossRefGoogle Scholar
  34. Moser LE, Vogel KP (1995) Switchgrass, big bluestem, and Indiangrass. In: Barnes RF, Miller DA, Nelson CJ (eds) Forages, vol 1., An introduction to grassland agriculture, Iowa State University Press, Ames, pp 409–420Google Scholar
  35. 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 8:925–935CrossRefGoogle Scholar
  36. Nageswara-Rao M, Soneji JR, Chen C, Huang S, Gmitter FG Jr (2008) Characterization of zygotic and nucellar seedlings from citrus rootstock candidates using RAPD and EST-SSR markers. Tree Genet Genomes 4:113–124CrossRefGoogle Scholar
  37. Nageswara-Rao M, Soneji JR, Kwit C, Stewart CN Jr (2013) Advances in biotechnology and genomics of switchgrass. Biotechnol Biofuels 6:77. doi: 10.1186/1754-6834-6-77 PubMedCentralPubMedCrossRefGoogle Scholar
  38. Narasimhamoorthy B, Saha MC, Swaller T, Bouton JH (2008) Genetic diversity in switchgrass collections assessed by EST-SSR markers. Bioenergy Res 1:136–146CrossRefGoogle Scholar
  39. Nei M (1972) Genetic distance between populations. Am Nat 106:283–292CrossRefGoogle Scholar
  40. Nei M (1973) Analysis of gene diversity in subdivided populations. Proc Natl Acad Sci USA 70:3321–3323PubMedCentralPubMedCrossRefGoogle Scholar
  41. Nielsen EL (1944) Analysis of variation in Panicum virgatum L. J Agric Res 69:327–353Google Scholar
  42. Pimm SL, Raven P (2000) Biodiversity: extinction by numbers. Nature 403:843–845PubMedCrossRefGoogle Scholar
  43. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959PubMedCentralPubMedGoogle Scholar
  44. Raghu S, Anderson RC, Daehler CC, Davis AS, Wiedenmann RN, Simberloff D, Mack RN (2006) Adding biofuels to the invasive species fire? Science 313:1742PubMedCrossRefGoogle Scholar
  45. Rajanikanth G, Nageswara-Rao M, Tambat B, Uma Shaanker R, Ganeshaiah KN, Kushalappa CG (2010) Are small forest fragments more heterogeneous among themselves than the large fragments? Biorem Biodivers Bioavailab 4:42–46Google Scholar
  46. Ravikanth G, Ganeshaiah KN, Uma Shaanker R (2002) Identification of hotspots of species richness and genetic variability in rattans: an approach using geographical information systems (GIS) and molecular tools. Plant Genet Resour Newsl 132:17–21Google Scholar
  47. Ridley CE, Jager HI, Clark CM, Efroymson RA, Kwit C, Landis DA, Leggett ZH, Miller DA (2013) Debate: can bioenergy be produced in a sustainable manner that protects biodiversity and avoids the risk of invaders? Bull Ecol Soc Am 94:277–290CrossRefGoogle Scholar
  48. Sang T, Crawford DJ, Stuessy TF (1997) Chloroplast DNA phylogeny, reticulate evolution, and biogeography of Paeonia (Paeoniaceae). Am J Bot 84:1120–1136PubMedCrossRefGoogle Scholar
  49. Selbo SM, Snow AA (2005) Flowering phenology and genetic similarity among local and recently introduced populations of Andropogon gerardii in Ohio. Restor Ecol 13:441–447CrossRefGoogle Scholar
  50. Shaw J, Lickey EB, Schilling EE, Small RL (2007) Comparison of whole chloroplast genome sequences to choose noncoding regions for phylogenetic studies in angiosperms: the tortoise and the hare III. Am J Bot 94:275–288PubMedCrossRefGoogle Scholar
  51. Sneath PHA, Sokal RR (1972) Numerical taxonomy: the principles and practice of numerical classification. WH Freeman, San FranciscoGoogle Scholar
  52. Statsoft (1993) Statistica ver 4.5. Statsoft Inc, TulsaGoogle Scholar
  53. Stottlemyer AL (2012) Investigating hybridization potential, components of fitness, and volunteerism in wild and cultivated Panicum virgatum L. (switchgrass). M.S. dissertation, The Ohio State UniversityGoogle Scholar
  54. Taberlet P, Gielly L, Pautou G, Bouvet J (1991) Universal primers for amplification of three noncoding regions of chloroplast DNA. Plant Mol Biol 17:1105–1109PubMedCrossRefGoogle Scholar
  55. Talbert LE, Timothy DH, Burns JC, Rawlings JO, Moll RH (1983) Estimates of genetic parameters in switchgrass. Crop Sci 23:725–728CrossRefGoogle Scholar
  56. Uma Shaanker R, Ganeshaiah KN, Nageswara-Rao M (2001) Genetic diversity of medicinal plant species in deciduous plants of India: impacts of harvesting and other anthropogenic pressures. J Plant Biol 28(1):91–97Google Scholar
  57. Vogel KP (2004) Switchgrass. In: Moser LE, Burson BL, Sollenberger LE (eds) Warm-season (C4) grasses. Agronomy monograph 45. ASA, CSSA, and SSSA, Madison, pp 561–588Google Scholar
  58. Wang X, Rinehart TA, Wadl PA, Spiers JM, Hadziabdic D, Windham MT, Trigiano RN (2009) A new electrophoresis technique to separate microsatellite alleles. Afr J Biotechnol 8:2432–2436Google Scholar
  59. Wang Z, Kenworthy KE, Wu Y (2010) Genetic diversity of common carpetgrass revealed by amplified fragment length polymorphism markers. Crop Sci 50:1366–1374CrossRefGoogle Scholar
  60. Wang YW, Samuels TD, Wu YQ (2011) Development of 1,030 genomic SSR markers in switchgrass. Theor Appl Genet 122:677–686PubMedCrossRefGoogle Scholar
  61. Warren JM, Raybould AF, Ball T, Gray AJ, Hayward MD (1998) Genetic structure in the perennial grasses Lolium perenne and Agrostis curtisii. Heredity 81:556–562CrossRefGoogle Scholar
  62. Wright L, Turhollow A (2010) Switchgrass selection as a “model” bioenergy crop: a history of the process. Biomass Bioenergy 34:851–868CrossRefGoogle Scholar
  63. Wu J, Vankat JL (1995) Island biogeography: theory and applications. In: Nierenberg WA (ed) Encyclopedia of environmental biology 2. Academic Press, San Diego, pp 371–379Google Scholar
  64. Wullschleger SD, Davis EB, Borsuk ME, Gunderson CA, Lynd LR (2010) Biomass production in switchgrass across the United States: database description and determinants of yield. Agron J 102:1158–1168CrossRefGoogle Scholar
  65. Yeh FC, Boyle TJB (1997) POPGENE Version 1.2 Microsoft window-based software for population genetics analysis. University of AlbertaGoogle Scholar
  66. Young AG, Boyle TJB (2000) Forest fragmentation. In: Young A, Boshier D, Boyle TJB (eds) Forest conservation and genetics—principles and practice. CABI, CSIRO, pp 123–134Google Scholar
  67. Zalapa JE, Price DL, Kaeppler SM, Tobias CM, Okada M, Casler MD (2011) Hierarchical classification of switchgrass using SSR and chloroplast sequences: ecotypes, ploidies, gene pools, and cultivars. Theor Appl Genet 122:805–817PubMedCrossRefGoogle Scholar
  68. Zeng C-L, Wang G-Y, Wang J-B, Yan G-X, Chen B-Y et al (2012) High-throughput discovery of chloroplast and mitochondrial DNA polymorphisms in Brassicaceae species by ORG-EcoTILLING. PLoS One 7(11):e47284. doi: 10.1371/journal.pone.0047284 PubMedCentralPubMedCrossRefGoogle Scholar
  69. Zhang Y, Zalapa JE, Jakubowski AR, Price DL, Acharya A, Wei Y, Brummer EC, Kaeppler SM, Casler MD (2011) Post-glacial evolution of Panicum virgatum: centers of diversity and gene pools revealed by SSR markers and cpDNA sequences. Genetica 139:933–948PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2014

Authors and Affiliations

  • Madhugiri Nageswara-Rao
    • 1
    • 2
  • Micaha Hanson
    • 1
  • Sujata Agarwal
    • 1
  • C. Neal StewartJr.
    • 1
    • 3
  • Charles Kwit
    • 1
    • 4
  1. 1.Department of Plant SciencesUniversity of TennesseeKnoxvilleUSA
  2. 2.Department of BiologyNew Mexico State UniversityLas CrucesUSA
  3. 3.BioEnergy Science CenterOak Ridge National LaboratoryOak RidgeUSA
  4. 4.Department of Forestry, Wildlife and FisheriesUniversity of TennesseeKnoxvilleUSA

Personalised recommendations