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

  • Sarah M. Ward (a1) and Marie Jasieniuk (a2)
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.

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Corresponding author's E-mail: sarah.ward@colostate.edu
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M. Agarwal , N. Shrivastava , and H. Padh 2008. Advances in molecular marker techniques and their applications in plant sciences. Plant Cell Rep. 27:617631.

O. Alberton , G. Kaschuk , and M. Hungria 2006. Sampling effects on the assessment of genetic diversity of rhizobia associated with soybean and common bean. Soil Biol. Biochem. 38:12981307.

J. M. Aparicio , J. Ortego , and P. J. Cordero 2006. What should we weigh to estimate heterozygosity, alleles or loci? Mol. Ecol. 15:46594665.

A. H. D. Brown 1989. Core collections: a practical approach to genetic resources management. Genome. 31:318324.

A. H. D. Brown , C. L. Brubaker , and J. L. Grace 1997. Regeneration of germplasm samples: wild vs. cultivated plant species. Crop Sci. 37:713.

J. D. Bussell 1999. The distribution of random amplified polymorphic DNA (RAPD) diversity amongst populations of Isotoma petraea (Lobeliaceae). Mol. Ecol. 8:775789.

S. Cavers , B. Degen , H. Caron , M. R. Lemes , R. Margis , F. Salgueiro , and A. J. Lowe 2005. Optimal sampling strategy for estimation of spatial genetic structure in tree populations. Heredity. 95:281289.

G. Charmet and F. Balfourier 1995. The use of geostatistics for sampling a core collection of perennial ryegrass populations. Genet. Res. Crop Evol. 42:303309.

S. Cozzolino , D. Cafasso , G. Pellegrino , A. Musacchio , and A. Widmer 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. 8:629639.

J. R. Ellis , C. H. Pashley , J. M. Buerke , and D. E. McCauley 2006. High genetic diversity in a rare and endangered sunflower as compared to a common congener. Mol. Ecol. 15:23452355.

B. K. Epperson and T. Li 1996. Measurement of genetic structure within populations using Moran's spatial autocorrelation statistics. Proc. Nat. Acad. Sci. U. S. A. 93:1052810532.

B. K. Epperson , Z. Huang , and T. Li 1999. Measures of spatial structure in samples of genotypes for multiallelic loci. Genet. Res. 73:251262.

A. Escudero , J. M. Iriondo , and M. E. Torres 2003. Spatial analysis of genetic diversity as a tool for plant conservation. Biol. Conserv. 113:351365.

G. Evanno , S. Regnaut , and J. Goudet 2005. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol. Ecol. 14:26112620.

L. Excoffier and G. Heckel 2006. Computer programs for population genetics data analysis: a survival guide. Nat. Rev. Genet. 7:745758.

D. Falush , M. Stephens , and J. K. Pritchard 2007. Inference of population structure using multilocus genotype data: dominant markers and null alleles. Mol. Ecol. Notes. 7:574578.

V. Fievet , P. Touzet , J. F. Arnaud , and J. Cuguen 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. 16:18471864.

M. Gaudeul , I. Till-Bottraud , F. Barjon , and S. Manel 2004. Genetic diversity and differentiation in Eryngium alpinum L. (Apiaceae): comparison of AFLP and microsatellite markers. Heredity. 92:508518.

N. Geleta , M. T. Labuschagne , and C. D. Viljoen 2006. Genetic diversity in sorghum germplasm as estimated by AFLP, SSR and morpho-agronomical markers. Biodivers. Conserv. 15:32513265.

C. Hallden , M. Hansen , N. O. Nilsson , A. Hjerdin , and T. Sall 1996. Competition as a source of error in RAPD analysis. Theor. Appl. Genet. 93:11851192.

J. L. Hamrick and M. J. Godt 1996. Effects of life history traits on genetic diversity in plant species. Phil. Trans. R. Soc. Lond. B. 351:12911298.

T. D. Harwood 2009. The circular definition of populations and its implication for biological sampling. Mol. Ecol. 18:765768.

M. Heckenberger , J. Muminovic , J. R. van der Voort , J. Peleman , M. Bohn , and A. E. Melchenger 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. 17:111125.

N. Isabel , J. Beaulieu , P. Theriault , and J. Bousquet 1999. Direct evidence for biased gene diversity estimates from dominant random amplified polymorphic DNA (RAPD) fingerprints. Mol. Ecol. 8:477483.

T. H. Jones , R. E. Vaillancourt , and B. M. Potts 2007. Detection and visualization of spatial genetic structure in continuous Eucalyptus globulus forest. Mol. Ecol. 16:697707.

L. Jost 2008. G ST and its relatives do not measure differentiation. Mol. Ecol. 17:40154026.

A. S. Jump and J. Penuelas 2007. Extensive spatial genetic structure revealed by AFLP but not SSR molecular markers in the wind-pollinated tree, Fagus sylvatica. Mol. Ecol. 16:925936.

S. T. Kalinowski 2002. How many alleles per locus should be used to estimate genetic distances? Heredity. 88:6265.

S. T. Kalinowski 2004. Counting alleles with rarefaction: private alleles and hierarchical sampling designs. Conserv. Genet. 5:539543.

S. T. Kalinowski 2005. Do polymorphic loci require large sample sizes to estimate genetic distances? Heredity. 94:3336.

A. Kumar and S. H. Rogstad 1998. A hierarchical analysis of minisatellite DNA diversity on Gambel oak (Quercus gambelii Nutt., Fagaceae). Mol. Ecol. 7:859869.

M. J. Lawrence , D. F. Marshall , and P. Davies 1995. Genetics of genetic conservation. I. Sample size when collecting germplasm. Euphytica. 84:8999.

P. L. Leberg 2002. Estimating allelic richness: effects of sample size and bottlenecks. Mol. Ecol. 11:24452449.

D. R. Lockwood , C. M. Richards , and G. M. Volk 2007. Probabilistic models for collecting genetic diversity: comparisons, caveats and limitations. Crop Sci. 47:861868.

M. Lynch and B. G. Milligan 1994. Analysis of population genetic structure with RAPD markers. Mol. Ecol. 3:9199.

S. Manel , F. Bertoud , E. Bellemain , M. Gaudeul , G. Luikart , J. E. Swenson , L. P. Waits , and P. Taberlet IntraBioDiv Consortium 2007. A new individual-based spatial approach for identifying genetic discontinuities in natural populations. Mol. Ecol. 16:20312043.

S. Manel , M. K. Schwarz , G. Luikart , and P. Taberlet 2003. Landscape genetics: combining landscape ecology and population genetics. Trends. Ecol. Evol. 18:189197.

S. Mariette , V. Le Corre , F. Austerlitz , and A. Kremer 2002. Sampling within the genome for measuring within-population diversity: trade-offs between markers. Mol. Ecol. 11:11451156.

C. E. McGregor , C. A. Lambert , M. M. Greyling , J. H. Louw , and L. Warnich 2000. A comparative assessment of DNA fingerprinting techniques (RAPD, ISSR, AFLP and SSR) in tetraploid potato (Solanum tuberosum L.) germplasm. Euphytica. 113:135144.

P. G. Meirmans and P. H. Van Tienderen 2004. GENOTYPE and GENODIVE: two programs for the analysis of genetic diversity of asexual organisms. Mol. Ecol. Notes. 4:792794.

M. C. Neel and M. P. Cummings 2003. Effectiveness of conservation targets in capturing genetic diversity. Cons. Biol. 17:219229.

M. Nei 1973. Analysis of gene diversity in subdivided populations. Proc. Nat. Acad. Sci. U. S. A. 70:33213323.

E. E. Nielsen , M. M. Hansen , and V. Loeschcke 1999. Genetic variation in time and space: microsatellite analysis of extinct and extant populations of Atlantic salmon. Evolution. 53:261268.

H. Nybom 2004. Comparison of different nuclear DNA markers for estimating intraspecific genetic diversity in plants. Mol. Ecol. 13:11431155.

M. Okada , R. Ahmad , and M. Jasieniuk 2007. Microsatellite variation points to local landscape plantings as sources of invasive pampas grass (Cortaderia selloana) in California. Mol. Ecol. 16:49564971.

M. Okada , B. J. Grewell , and M. Jasieniuk 2009. Clonal spread of invasive Ludwigia hexapetala and L. grandiflora in freshwater wetlands of California. Aquatic Bot. 91:123129.

O. Ozbek , E. Millet , Y. Anikster , O. Arslan , and M. Feldman 2007. Spatio-temporal variation in populations of wild emmer wheat, Triticum turgidum ssp. dicoccoides, as revealed by AFLP analysis. Theor. Appl. Genet. 115:1926.

H. Ozkan , S. Kafkas , M. S. Ozer , and A. Bartolini 2005. Genetic relationships among south-east Turkey wild barley populations and sampling strategies of Hordeum spontaneum . Theor. Appl. Genet. 112:1220.

R. J. Petit , J. Duminil , S. Fineschi , A. Hampe , D. Salvini , and G. G. Vendramin 2005. Comparative organization of chloroplast, mitochondrial and nuclear diversity in plant populations. Mol. Ecol. 14:689701.

C. M. Richards , M. F. Antolin , A. Reilley , J. Poole , and C. Walters 2007. Capturing genetic diversity of wild populations for ex situ conservation: Texas wild rice (Zizania texana) as a model. Genet. Resour. Crop Evol. 54:837848.

K. Saltonstall 2002. Cryptic invasion by a non-native genotype of the common reed, Phragmites australis, into North America. Proc. Natl. Acad. Sci. U. S. A. 99:24452449.

R. L. Sapra , P. Narim , S. V. S. Chauhan , S. K. Lal , and B. B. Singh 2003. Sample size for collecting germplasms—a polyploid model with mixed mating system. J. Biosci. 28:155161.

J. F. Scheepens , R. M. Veeneklaas , L. Van de Zande , and J. P. Bakker 2007. Clonal structure of Elytrigia atherica along different successional stages of a salt marsh. Mol. Ecol. 16:11151124.

D. J. Schoen and A. H. D. Brown 2001. The conservation of wild plant species in seed banks. BioScience. 51:960966.

M. Singh , K. Chabane , J. Valkoun , and T. Blake 2006. Optimum sample size for estimating gene diversity in wild wheat using AFLP markers. Genet. Resour. Crop Evol. 53:2333.

P. E. Smouse and R. Peakall 1999. Spatial autocorrelation analysis of individual multiallele and multilocus genetic structure. Heredity. 82:561573.

J. E. Staub , Y. Danin-Poleg , G. Fazio , Y. Horejsi , N. Reis , and N. Katsir 2000. Comparative analysis of melon (Cucumis melo L.) using random amplified polymorphic DNA and simple sequence repeat markers. Euphytica. 115:225241.

A. Storfer , M. A. Murphy , J. S. Evans , C. S. Goldberg , S. Robinson , S. F. Spear , R. Dezzani , E. Delmelle , L. Vierling , and L. P. Waits 2007. Putting the ‘landscape’ in landscape genetics. Heredity. 98:128142.

J-I. Suzuki , T. Herben , and M. Maki 2004. An under-appreciated difficulty: sampling of plant populations for analysis using molecular markers. Evol. Ecol. 18:625646.

S. Tang , W. Dai , M. Li , Y. Zhang , Y. Geng , L. Wang , and Y. Zhong 2008. Genetic diversity of relictual and endangered plant Abies ziyuanensis (Pinaceae) revealed by AFLP and SSR markers. Genetica. 133:2130.

T. Torimaru , M. Tomaru , N. Nishimura , and S. Yamamoto 2003. Clonal diversity and genetic differentiation in Ilex leucoclada M. patches in an old-growth beech forest. Mol. Ecol. 12:809818.

M. E. Turner , J. C. Stephens , and W. W. Anderson 1982. Homozygosity and patch structure in plant populations as a result of nearest-neighbor pollination. Proc. Natl. Acad. Sci. U. S. A. 79:203207.

S. Wahlund 1928. Zusammensetzung von Populationen und Korrelation-serscheinungen von Standpunkt der Verbungslehre aus betrachtet. Hereditas. 11:65106.

R. S. Waples and O. Gaggiotti 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. 15:14191439.

S. M. Ward 2006a. Genetic analysis of invasive plant populations at different spatial scales. Biol. Invasions. 8:541552.

S. M. Ward , S. D. Reid , J. Harrington , J. R. Sutton , and K. G. Beck 2008. Genetic diversity in invasive populations of yellow toadflax (Linaria vulgaris Miller) in the western United States. Weed Sci. 56:394399.

B. S. Weir and C. C. Cockerham 1984. Estimating F-statistics for the analysis of population structure. Evolution. 38:13581370.

K. H. Wolfe , W. H. Li , and P. M. Sharp 1987. Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs. Proc. Natl. Acad. Sci. U. S. A. 84:90549058.

M. Woodhead , J. Russell , J. Squirrell , P. M. Hollingsworth , K. Mackenzie , M. Gibby , and W. Powells 2005. Comparative analysis of population genetic structure in Athyrium distentifolium (Pteridophyta) using AFLPs and SSRs from anonymous and transcribed regions. Mol. Ecol. 14:16811695.

S. Wright 1951. The genetical structure of populations. Ann. Eugenics. 15:323354.

K. Yonezawa 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. 34:345354.

R. Zhao , Z. Cheng , W. Lu , and B. Lu 2006. Estimating genetic diversity and sampling strategy for a wild soybean (Glycine soja) population based on different molecular markers. Chinese Sci. Bull. 51:12191227.

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  • ISSN: 0043-1745
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