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Review: Sampling Weedy and Invasive Plant Populations for Genetic Diversity Analysis

Published online by Cambridge University Press:  20 January 2017

Sarah M. Ward  and
Marie Jasieniuk
Sarah M. Ward*
Affiliation:
Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523
Marie Jasieniuk
Affiliation:
Department of Plant Sciences, University of California, Davis, CA 95616
*
Corresponding author's E-mail: [email protected]
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Abstract

Recent advances in molecular methods and statistical analyses provide weed scientists with powerful tools for examining the genetic structure of weedy plant populations. The value of these studies depends on effective sampling protocols; however, there is little consensus on how to sample plant populations for genetic diversity analyses. In this review, we draw on published literature that incorporates sampling theory and spatial statistics in population genetic analyses to identify key factors to consider when designing a sampling strategy. We discuss how sampling design is affected by research objectives, biology of the study species, population structure, marker choice, and the genetic parameters to be investigated, and we offer suggestions on defining sampling units and developing sampling protocols.

Keywords

AFLPgenetic diversity analysisISSRmolecular markerspopulation geneticsRAPDsamplingSSR
Type
Weed Biology and Ecology
Information
Weed Science , Volume 57 , Issue 6 , December 2009 , pp. 593 - 602
Copyright
Copyright © Weed Science Society of America 

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References

Literature Cited

Agarwal, M., Shrivastava, N., and Padh, H. 2008. Advances in molecular marker techniques and their applications in plant sciences. Plant Cell Rep. 27:617–631.Google Scholar
Alberton, O., Kaschuk, G., and Hungria, M. 2006. Sampling effects on the assessment of genetic diversity of rhizobia associated with soybean and common bean. Soil Biol. Biochem. 38:1298–1307.Google Scholar
Aparicio, J. M., Ortego, J., and Cordero, P. J. 2006. What should we weigh to estimate heterozygosity, alleles or loci? Mol. Ecol. 15:4659–4665.CrossRefGoogle ScholarPubMed
Birky, C. W., Fuerst, P., and Maruyama, T. 1989. Organelle gene diversity under migration, mutation and drift: equilibrium expectations, approach to equilibrium effects of heteroplasmic cells, and comparison to nuclear genes. Genetics. 121:613–627.Google Scholar
Brown, A. H. D. 1989. Core collections: a practical approach to genetic resources management. Genome. 31:318–324.CrossRefGoogle Scholar
Brown, A. H. D. and Biggs, J. D. 1991. Sampling strategies for genetic variation in ex situ collections of endangered plant species. Pages 165–191. In Falk, D. A. and Williams, J. T. Genetics and Conservation of Rare Plants. New York Oxford University Press.Google Scholar
Brown, A. H. D., Brubaker, C. L., and Grace, J. L. 1997. Regeneration of germplasm samples: wild vs. cultivated plant species. Crop Sci. 37:7–13.Google Scholar
Brown, A. H. D. and Marshall, D. R. 1995. A basic sampling strategy: theory and practice. Pages 75–91. In Guarino, L. Collecting Plant Genetic Diversity: Technical Guidelines. Wallingford, UK CABI.Google Scholar
Bussell, J. D. 1999. The distribution of random amplified polymorphic DNA (RAPD) diversity amongst populations of Isotoma petraea (Lobeliaceae). Mol. Ecol. 8:775–789.CrossRefGoogle Scholar
Cavers, S., Degen, B., Caron, H., Lemes, M. R., Margis, R., Salgueiro, F., and Lowe, A. J. 2005. Optimal sampling strategy for estimation of spatial genetic structure in tree populations. Heredity. 95:281–289.CrossRefGoogle ScholarPubMed
Charmet, G. and Balfourier, F. 1995. The use of geostatistics for sampling a core collection of perennial ryegrass populations. Genet. Res. Crop Evol. 42:303–309.Google Scholar
Cozzolino, S., Cafasso, D., Pellegrino, G., Musacchio, A., and Widmer, A. 2007. Genetic variation in time and space: the use of herbarium specimens to reconstruct patterns of genetic variation in the endangered orchid Anacamptis palustris . Conserv. Genet. 8:629–639.CrossRefGoogle Scholar
De Gruijter, J., Brus, D., Bierkens, M., and Knotters, M. 2006. Sampling for Natural Resource Monitoring. New York Springer. 332.CrossRefGoogle Scholar
Ellis, J. R., Pashley, C. H., Buerke, J. M., and McCauley, D. E. 2006. High genetic diversity in a rare and endangered sunflower as compared to a common congener. Mol. Ecol. 15:2345–2355.Google Scholar
Epperson, B. K. 1990. Spatial patterns of genetic variation within plant populations. Pages 229–253. In Brown, A. H. D., Clegg, M. T., Kahler, A. L., and Weir, B. S. Plant Population Genetics, Breeding, and Genetic Resources. Sunderland, MA Sinauer.Google Scholar
Epperson, B. K. and Li, T. 1996. Measurement of genetic structure within populations using Moran's spatial autocorrelation statistics. Proc. Nat. Acad. Sci. U. S. A. 93:10528–10532.Google Scholar
Epperson, B. K., Huang, Z., and Li, T. 1999. Measures of spatial structure in samples of genotypes for multiallelic loci. Genet. Res. 73:251–262.Google Scholar
Escudero, A., Iriondo, J. M., and Torres, M. E. 2003. Spatial analysis of genetic diversity as a tool for plant conservation. Biol. Conserv. 113:351–365.Google Scholar
Evanno, G., Regnaut, S., and Goudet, J. 2005. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol. Ecol. 14:2611–2620.Google Scholar
Excoffier, L. and Heckel, G. 2006. Computer programs for population genetics data analysis: a survival guide. Nat. Rev. Genet. 7:745–758.CrossRefGoogle ScholarPubMed
Excoffier, L., Smouse, P. E., and Quattro, J. M. 1992. Analysis of molecular variance inferred from metric distances among DNA haplotypes: applications to human mitochondrial DNA restriction data. Genetics. 131:479–491.Google Scholar
Falush, D., Stephens, M., and Pritchard, J. K. 2003. Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics. 164:1567–1587.Google Scholar
Falush, D., Stephens, M., and Pritchard, J. K. 2007. Inference of population structure using multilocus genotype data: dominant markers and null alleles. Mol. Ecol. Notes. 7:574–578.Google Scholar
Fievet, V., Touzet, P., Arnaud, J. F., and Cuguen, J. 2007. Spatial analysis of nuclear and cytoplasmic DNA diversity in wild sea beet (Beta vulgaris ssp. maritima) populations: do marine currents shape the genetic structure? Mol. Ecol. 16:1847–1864.Google Scholar
Gaskin, J. F. 2006. Clonal structure of invasive hoary cress (Lepidium draba) infestations. Weed Sci. 54:428–434.Google Scholar
Gaudeul, M., Till-Bottraud, I., Barjon, F., and Manel, S. 2004. Genetic diversity and differentiation in Eryngium alpinum L. (Apiaceae): comparison of AFLP and microsatellite markers. Heredity. 92:508–518.Google Scholar
Geleta, N., Labuschagne, M. T., and Viljoen, C. D. 2006. Genetic diversity in sorghum germplasm as estimated by AFLP, SSR and morpho-agronomical markers. Biodivers. Conserv. 15:3251–3265.CrossRefGoogle Scholar
Hale, A. L., Farnham, M. W., and Menz, M. A. 2006. Use of PCR-based markers for differentiating elite broccoli inbreds. J. Am. Soc. Hort. Sci. 131:418–423.Google Scholar
Hallden, C., Hansen, M., Nilsson, N. O., Hjerdin, A., and Sall, T. 1996. Competition as a source of error in RAPD analysis. Theor. Appl. Genet. 93:1185–1192.Google Scholar
Hamrick, J. L. and Godt, M. J. 1983. The distribution of genetic variation within and among natural plant populations. Pages 335–348. In Shonewald-Cox, C. M., Chambers, S. M., MacBryde, B., and Thomas, L. Genetics and Conservation. Menlo Park, CA Cummings.Google Scholar
Hamrick, J. L. and Godt, M. J. 1996. Effects of life history traits on genetic diversity in plant species. Phil. Trans. R. Soc. Lond. B. 351:1291–1298.Google Scholar
Harwood, T. D. 2009. The circular definition of populations and its implication for biological sampling. Mol. Ecol. 18:765–768.Google Scholar
Heckenberger, M., Muminovic, J., van der Voort, J. R., Peleman, J., Bohn, M., and Melchenger, A. E. 2006. Identification of essentially derived varieties obtained from biparental crosses of homozygous lines. III. AFLP data from maize inbreds and comparison with SSR data. Mol. Breeding. 17:111–125.Google Scholar
Ignjatovic-Micic, D., Drinic, S. M., Nikolic, A., and Lazic-Jacinic, V. 2007. Comparison of AFLP and SSR markers for genetic diversity studies in maize populations. Maydica. 52:399–406.Google Scholar
Isabel, N., Beaulieu, J., Theriault, P., and Bousquet, J. 1999. Direct evidence for biased gene diversity estimates from dominant random amplified polymorphic DNA (RAPD) fingerprints. Mol. Ecol. 8:477–483.Google Scholar
Iz, B., Maquet, A., Degreef, J., Wathelet, B., and Baudoin, J. P. 1998. Sample size for collecting seeds in germplasm conservation: the case of the lima bean (Phaseolus lunatus L.) Theor. Appl. Genet. 97:187–194.Google Scholar
Jasieniuk, M. and Maxwell, B. D. 2001. Plant diversity: new insights from molecular biology and genomics technologies. Weed Sci. 49:257–265.CrossRefGoogle Scholar
Jones, T. H., Vaillancourt, R. E., and Potts, B. M. 2007. Detection and visualization of spatial genetic structure in continuous Eucalyptus globulus forest. Mol. Ecol. 16:697–707.Google Scholar
Jost, L. 2008. G ST and its relatives do not measure differentiation. Mol. Ecol. 17:4015–4026.Google Scholar
Jump, A. S. and Penuelas, J. 2007. Extensive spatial genetic structure revealed by AFLP but not SSR molecular markers in the wind-pollinated tree, Fagus sylvatica. Mol. Ecol. 16:925–936.Google Scholar
Kalinowski, S. T. 2002. How many alleles per locus should be used to estimate genetic distances? Heredity. 88:62–65.Google Scholar
Kalinowski, S. T. 2004. Counting alleles with rarefaction: private alleles and hierarchical sampling designs. Conserv. Genet. 5:539–543.Google Scholar
Kalinowski, S. T. 2005. Do polymorphic loci require large sample sizes to estimate genetic distances? Heredity. 94:33–36.Google Scholar
Krebs, C. J. 1999. Ecological Methodology. Menlo Park, CA Cummings. 620.Google Scholar
Kumar, A. and Rogstad, S. H. 1998. A hierarchical analysis of minisatellite DNA diversity on Gambel oak (Quercus gambelii Nutt., Fagaceae). Mol. Ecol. 7:859–869.Google Scholar
Lawrence, M. J., Marshall, D. F., and Davies, P. 1995. Genetics of genetic conservation. I. Sample size when collecting germplasm. Euphytica. 84:89–99.Google Scholar
Leberg, P. L. 2002. Estimating allelic richness: effects of sample size and bottlenecks. Mol. Ecol. 11:2445–2449.Google Scholar
Lockwood, D. R., Richards, C. M., and Volk, G. M. 2007. Probabilistic models for collecting genetic diversity: comparisons, caveats and limitations. Crop Sci. 47:861–868.Google Scholar
Lowe, A., Harris, S., and Ashton, P. 2004. Ecological Genetics: Design, Analysis and Application. Oxford, UK Blackwell. 326.Google Scholar
Lynch, M. and Milligan, B. G. 1994. Analysis of population genetic structure with RAPD markers. Mol. Ecol. 3:91–99.Google Scholar
Manel, S., Bertoud, F., Bellemain, E., Gaudeul, M., Luikart, G., Swenson, J. E., Waits, L. P., and Taberlet, P. IntraBioDiv Consortium 2007. A new individual-based spatial approach for identifying genetic discontinuities in natural populations. Mol. Ecol. 16:2031–2043.Google Scholar
Manel, S., Schwarz, M. K., Luikart, G., and Taberlet, P. 2003. Landscape genetics: combining landscape ecology and population genetics. Trends. Ecol. Evol. 18:189–197.Google Scholar
Mariette, S., Le Corre, V., Austerlitz, F., and Kremer, A. 2002. Sampling within the genome for measuring within-population diversity: trade-offs between markers. Mol. Ecol. 11:1145–1156.Google Scholar
Marshall, D. R. and Brown, A. H. D. 1975. Optimum sampling strategies in genetic conservation. Pages 53–80. In Frankel, O. and Hawkes, J. Crop Genetic Resources for Today and Tomorrow. Cambridge, UK Cambridge University Press.Google Scholar
McGregor, C. E., Lambert, C. A., Greyling, M. M., Louw, J. H., and Warnich, L. 2000. A comparative assessment of DNA fingerprinting techniques (RAPD, ISSR, AFLP and SSR) in tetraploid potato (Solanum tuberosum L.) germplasm. Euphytica. 113:135–144.Google Scholar
Meirmans, P. G. and Van Tienderen, P. H. 2004. GENOTYPE and GENODIVE: two programs for the analysis of genetic diversity of asexual organisms. Mol. Ecol. Notes. 4:792–794.Google Scholar
Muirhead, J. R., Gray, D. K., Kelly, D. W., Ellis, S. M., Heath, D. D., and MacIsaac, H. J. 2008. Identifying the source of species invasions: sampling intensity vs. genetic identity. Mol. Ecol. 17:1020–1035.Google Scholar
Neel, M. C. and Cummings, M. P. 2003. Effectiveness of conservation targets in capturing genetic diversity. Cons. Biol. 17:219–229.Google Scholar
Nei, M. 1973. Analysis of gene diversity in subdivided populations. Proc. Nat. Acad. Sci. U. S. A. 70:3321–3323.Google Scholar
Nei, M. 1978. Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics. 89:583–590.Google Scholar
Nei, M. and Kumar, S. 2000. Molecular Evolution and Phylogenetics. Oxford, UK Oxford University Press. 333.Google Scholar
Nielsen, E. E., Hansen, M. M., and Loeschcke, V. 1999. Genetic variation in time and space: microsatellite analysis of extinct and extant populations of Atlantic salmon. Evolution. 53:261–268.Google Scholar
Nybom, H. 2004. Comparison of different nuclear DNA markers for estimating intraspecific genetic diversity in plants. Mol. Ecol. 13:1143–1155.Google Scholar
Okada, M., Ahmad, R., and Jasieniuk, M. 2007. Microsatellite variation points to local landscape plantings as sources of invasive pampas grass (Cortaderia selloana) in California. Mol. Ecol. 16:4956–4971.Google Scholar
Okada, M., Grewell, B. J., and Jasieniuk, M. 2009. Clonal spread of invasive Ludwigia hexapetala and L. grandiflora in freshwater wetlands of California. Aquatic Bot. 91:123–129.Google Scholar
Ozbek, O., Millet, E., Anikster, Y., Arslan, O., and Feldman, M. 2007. Spatio-temporal variation in populations of wild emmer wheat, Triticum turgidum ssp. dicoccoides, as revealed by AFLP analysis. Theor. Appl. Genet. 115:19–26.Google Scholar
Ozkan, H., Kafkas, S., Ozer, M. S., and Bartolini, A. 2005. Genetic relationships among south-east Turkey wild barley populations and sampling strategies of Hordeum spontaneum . Theor. Appl. Genet. 112:12–20.Google Scholar
Petit, R. J., Duminil, J., Fineschi, S., Hampe, A., Salvini, D., and Vendramin, G. G. 2005. Comparative organization of chloroplast, mitochondrial and nuclear diversity in plant populations. Mol. Ecol. 14:689–701.Google Scholar
Pons, O. and Petit, R. J. 1996. Measuring and testing genetic differentiation with ordered versus unordered alleles. Genetics. 144:1237–1245.Google Scholar
Pritchard, J. K., Stephens, M., and Donnelly, P. 2000. Inference of population structure using multilocus genotype data. Genetics. 155:945–959.CrossRefGoogle ScholarPubMed
Richards, C. M., Antolin, M. F., Reilley, A., Poole, J., and Walters, C. 2007. Capturing genetic diversity of wild populations for ex situ conservation: Texas wild rice (Zizania texana) as a model. Genet. Resour. Crop Evol. 54:837–848.Google Scholar
Saltonstall, K. 2002. Cryptic invasion by a non-native genotype of the common reed, Phragmites australis, into North America. Proc. Natl. Acad. Sci. U. S. A. 99:2445–2449.Google Scholar
Sapra, R. L., Narim, P., Chauhan, S. V. S., Lal, S. K., and Singh, B. B. 2003. Sample size for collecting germplasms—a polyploid model with mixed mating system. J. Biosci. 28:155–161.Google Scholar
Scheepens, J. F., Veeneklaas, R. M., Van de Zande, L., and Bakker, J. P. 2007. Clonal structure of Elytrigia atherica along different successional stages of a salt marsh. Mol. Ecol. 16:1115–1124.Google Scholar
Schoen, D. J. and Brown, A. H. D. 2001. The conservation of wild plant species in seed banks. BioScience. 51:960–966.Google Scholar
Singh, M., Chabane, K., Valkoun, J., and Blake, T. 2006. Optimum sample size for estimating gene diversity in wild wheat using AFLP markers. Genet. Resour. Crop Evol. 53:23–33.Google Scholar
Smouse, P. E. and Peakall, R. 1999. Spatial autocorrelation analysis of individual multiallele and multilocus genetic structure. Heredity. 82:561–573.Google Scholar
Staub, J. E., Danin-Poleg, Y., Fazio, G., Horejsi, Y., Reis, N., and Katsir, N. 2000. Comparative analysis of melon (Cucumis melo L.) using random amplified polymorphic DNA and simple sequence repeat markers. Euphytica. 115:225–241.Google Scholar
Storfer, A., Murphy, M. A., Evans, J. S., Goldberg, C. S., Robinson, S., Spear, S. F., Dezzani, R., Delmelle, E., Vierling, L., and Waits, L. P. 2007. Putting the ‘landscape’ in landscape genetics. Heredity. 98:128–142.Google Scholar
Suzuki, J-I., Herben, T., and Maki, M. 2004. An under-appreciated difficulty: sampling of plant populations for analysis using molecular markers. Evol. Ecol. 18:625–646.Google Scholar
Tang, S., Dai, W., Li, M., Zhang, Y., Geng, Y., Wang, L., and Zhong, Y. 2008. Genetic diversity of relictual and endangered plant Abies ziyuanensis (Pinaceae) revealed by AFLP and SSR markers. Genetica. 133:21–30.Google Scholar
Torimaru, T., Tomaru, M., Nishimura, N., and Yamamoto, S. 2003. Clonal diversity and genetic differentiation in Ilex leucoclada M. patches in an old-growth beech forest. Mol. Ecol. 12:809–818.Google Scholar
Turner, M. E., Stephens, J. C., and Anderson, W. W. 1982. Homozygosity and patch structure in plant populations as a result of nearest-neighbor pollination. Proc. Natl. Acad. Sci. U. S. A. 79:203–207.Google Scholar
Volk, G. M., Lockwood, D. R., and Richards, C. M. 2007. Wild plant sampling strategies: the roles of ecology and evolution. Plant Breeding Rev. 29:285–313.Google Scholar
Wahlund, S. 1928. Zusammensetzung von Populationen und Korrelation-serscheinungen von Standpunkt der Verbungslehre aus betrachtet. Hereditas. 11:65–106.Google Scholar
Waples, R. S. and Gaggiotti, O. 2006. What is a population? An empirical evaluation of some genetic methods for identifying the number of gene pools and their degree of connectivity. Mol. Ecol. 15:1419–1439.Google Scholar
Ward, S. M. 2006a. Genetic analysis of invasive plant populations at different spatial scales. Biol. Invasions. 8:541–552.Google Scholar
Ward, S. M. 2006b. Molecular marker and DNA sequencing methods. Pages 347–369. In Motley, T. J. and Cross, H. Darwin's Harvest. New York Columbia University Press.Google Scholar
Ward, S. M., Reid, S. D., Harrington, J., Sutton, J. R., and Beck, K. G. 2008. Genetic diversity in invasive populations of yellow toadflax (Linaria vulgaris Miller) in the western United States. Weed Sci. 56:394–399.Google Scholar
Weir, B. S. and Cockerham, C. C. 1984. Estimating F-statistics for the analysis of population structure. Evolution. 38:1358–1370.Google Scholar
Wolfe, K. H., Li, W. H., and Sharp, P. M. 1987. Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs. Proc. Natl. Acad. Sci. U. S. A. 84:9054–9058.Google Scholar
Woodhead, M., Russell, J., Squirrell, J., Hollingsworth, P. M., Mackenzie, K., Gibby, M., and Powells, W. 2005. Comparative analysis of population genetic structure in Athyrium distentifolium (Pteridophyta) using AFLPs and SSRs from anonymous and transcribed regions. Mol. Ecol. 14:1681–1695.Google Scholar
Wright, S. 1943. Isolation by distance. Genetics. 28:114–138.Google Scholar
Wright, S. 1951. The genetical structure of populations. Ann. Eugenics. 15:323–354.Google Scholar
Yonezawa, K. 1985. A definition of the optimal allocation of effort in conservation of plant genetic resources with application to sample size determination for field collection. Euphytica. 34:345–354.Google Scholar
Zhao, R., Cheng, Z., Lu, W., and Lu, B. 2006. Estimating genetic diversity and sampling strategy for a wild soybean (Glycine soja) population based on different molecular markers. Chinese Sci. Bull. 51:1219–1227.Google Scholar