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Use of AFLP Markers to Assess Genetic Diversity in Palmer Amaranth (Amaranthus palmeri) Populations from North Carolina and Georgia

Published online by Cambridge University Press:  20 January 2017

Aman Chandi ,
Susana R. Milla-Lewis ,
David L. Jordan ,
Alan C. York ,
James D. Burton ,
M. Carolina Zuleta ,
Jared R. Whitaker  and
A. Stanley Culpepper
Aman Chandi
Affiliation:
Department of Crop Science, North Carolina State University, Box 7620, Raleigh, NC 27695
Susana R. Milla-Lewis
Affiliation:
Department of Crop Science, North Carolina State University, Box 7620, Raleigh, NC 27695
David L. Jordan*
Affiliation:
Department of Crop Science, North Carolina State University, Box 7620, Raleigh, NC 27695
Alan C. York
Affiliation:
Department of Crop Science, North Carolina State University, Box 7620, Raleigh, NC 27695
James D. Burton
Affiliation:
Department of Horticultural Science, North Carolina State University, Box 7609, Raleigh, NC 27695
M. Carolina Zuleta
Affiliation:
Department of Crop Science, North Carolina State University, Box 7620, Raleigh, NC 27695
Jared R. Whitaker
Affiliation:
Department of Crop Science, North Carolina State University, Box 7620, Raleigh, NC 27695
A. Stanley Culpepper
Affiliation:
University of Georgia, P.O. Box 748, Tifton, GA 31794
*
Corresponding author's E-mail: [email protected]
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Abstract

Glyphosate-resistant Palmer amaranth is a serious problem in southern cropping systems. Much phenotypic variation is observed in Palmer amaranth populations with respect to plant growth and development and susceptibility to herbicides. This may be related to levels of genetic diversity existing in populations. Knowledge of genetic diversity in populations of Palmer amaranth may be useful in understanding distribution and development of herbicide resistance. Research was conducted to assess genetic diversity among and within eight Palmer amaranth populations collected from North Carolina and Georgia using amplified fragment length polymorphism (AFLP) markers. Pair-wise genetic similarity (GS) values were found to be relatively low, averaging 0.34. The highest and the lowest GS between populations were 0.49 and 0.24, respectively, while the highest and the lowest GS within populations were 0.56 and 0.36, respectively. Cluster and principal coordinate (PCO) analyses grouped individuals mostly by population (localized geographic region) irrespective of response to glyphosate or gender of individuals. Analysis of molecular variance (AMOVA) results when populations were nested within states revealed significant variation among and within populations within states while variation among states was not significant. Variation among and within populations within state accounted for 19 and 77% of the total variation, respectively, while variation among states accounted for only 3% of the total variation. The within population contribution towards total variation was always higher than among states and among populations within states irrespective of response to glyphosate or gender of individuals. These results are significant in terms of efficacy of similar management approaches both in terms of chemical and biological control in different areas infested with Palmer amaranth.

Keywords

Palmer amaranth, Amaranthus palmeri S. WatsGlyphosateherbicide resistancephenotypic variation
Type
Weed Biology and Ecology
Information
Weed Science , Volume 61 , Issue 1 , March 2013 , pp. 136 - 145
Copyright
Copyright © Weed Science Society of America 

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Footnotes

current address: University of Georgia, P.O. Box 8112, Statesboro, GA 30460.

References

Literature Cited

Afanador, L. K., Haley, S. D., and Kelly, J. D. 1993. Adoption of a “mini-prep” DNA extraction method for RAPD marker analysis in common bean (Phaseolus vulgaris L.). Annu. Rep. Bean Improv. Coop. 36: 10–11.Google Scholar
Andersen, J. A., Churchill, G. A., Autrique, J. E., Tanksley, S. D., and Sorrells, M. E. 1993. Optimizing parental selection for genetic linkage maps. Genome. 36: 181–186.Google Scholar
Barrett, R. D. H. and Schluter, D. 2008. Adaptation from standing genetic variation. Trends Eco. Evol. 23: 38–44.Google Scholar
Bond, J. A. and Oliver, L. R. 2006. Comparative growth of Palmer amaranth (Amaranthus palmeri) accessions. Weed Sci. 54: 121–126.Google Scholar
Botstein, D., White, R. L., Skolnick, M., and Davis, R. W. 1980. Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am. J. Hum. Genet. 32: 314–331.Google Scholar
Burgos, N. R., Kuk, Y., and Talbert, R. E. 2001. Amaranthus palmeri resistance and differential tolerance of Amaranthus palmeri and Amaranthus hybridus to ALS-inhibiting herbicides. Pestic. Manag. Sci. 57: 449–457.Google Scholar
Caballero, A., Quesada, H., and Alvarez, E. R. 2008. Impact of amplified fragment length polymorphism size homoplasy on the estimation of population genetic diversity and the detection of selective loci. Genetics. 179: 539–554.Google Scholar
Chan, K. F. and Sun, M. 1997. Genetic diversity and relationships detected by isozyme and RAPD analysis of crop and wild species of Amaranthus . Thoer. Appl. Genet. 95: 865–873.Google Scholar
Coulibaly, S., Pasquet, R. S., Papa, R., and Gepts, P. 2002. AFLP analysis of the phonetic organization and genetic diversity of Vigna unguiculata L. Walp. reveals extensive gene flow between wild and domesticated types. Theor. Appl. Genet. 104: 358–366.Google Scholar
Culpepper, A. S., Whitaker, J. R., MacRae, A. W., and York, A. C. 2008. Distribution of glyphosate-resistant Palmer amaranth (Amaranthus palmeri) in Georgia and North Carolina during 2005 and 2006. J. Cotton Sci. 12: 306–310.Google Scholar
d'Ennequin, M. L. T., Panuad, O., and Toupance, B. 2000. Assessment of genetic relationship between Setaria italica and its wild relative S. viridis using AFPL markers. Theor. Appl. Genet. 100: 1061–1066.Google Scholar
Dice, L. R. 1945. Measures of the amount of ecologic association between species. Ecology. 26: 297–302.Google Scholar
Esfahani, S. T., Shiran, B., and Balali, G. 2009. AFLP markers for the assessment of genetic diversity in European and North American potato varieties cultivated in Iran. Crop Breed. Appl. Biotechnol. 9: 75–86.Google Scholar
Fernald, M. L. 1950. Gray's Manual of Botany. 8th ed. New York: American Book Co. 602 p.Google Scholar
Garcia-Mas, J., Oliver, M., Gómez-Paniagua, H., and de Vicente, M. C. 2000. Comparing AFLP, RAPD, and RFLP markers for measuring genetic diversity in melon. Thoer. Appl. Genet. 101: 860–864.Google Scholar
Garvey, P. V. 1999. Goosegrass (Eleusine indica) and Palmer amaranth (Amaranthus palmeri) interference in plasticulture tomato. Ph.D Dissertation. Raleigh, NC: North Carolina State University. 101 p.Google Scholar
Geuna, F., Toschi, M., and Bassi, D. 2003. The use of AFLP markers for cultivar identification in apricot. Plant Breed. 122: 526–531.Google Scholar
Gossett, B. J., Murdock, E. C., and Toler, J. E. 1992. Resistance of Palmer amaranth (Amaranthus palmeri) to the dinitroaniline herbicides. Weed Technol. 6: 587–591.Google Scholar
Harper, J. L. 1977. Population Biology of Plants. San Diego, CA: Academic Press. 892 p.Google Scholar
Heap, I. 2012. The International Survey of Herbicide Resistant Weeds. http://www.wssa.net. Accessed: January 2, 2012.Google Scholar
Holt, J. S. 1992. History of identification of herbicide-resistant weeds. Weed Technol. 6: 615–620.Google Scholar
Holt, J. S. and LeBaron, H. M. 1990. Significance and distribution of herbicide resistance. Weed Technol. 4: 141–149.Google Scholar
Hongtrakul, V., Huestis, G. M., and Knapp, S. J. 1997. Amplified fragment length polymorphisms as a tool for DNA fingerprinting sunflower germplasm: genetic diversity among oilseed inbred lines. Theor. Appl. Genet. 95: 400–407.Google Scholar
Horak, M. J. and Peterson, D. E. 1995. Populations of Palmer amaranth (Amaranthus palmeri) and common waterhemp (Amaranthus rudis) are resistant to imazethapyr and thifensulfuron. Weed Technol. 9: 192–195.Google Scholar
Ilgin, M., Kafkas, S., and Ercisli, S. 2009. Molecular characterization of plum cultivars by AFLP markers. Biotechnol. & Biotechnol. Eq. 23: 1189–1193.Google Scholar
Jha, P., Norsworthy, J. K., Malik, M. S., Bangarwa, S. K., and Oliveira, M. J. 2006. Temporal emergence of Palmer amaranth from a natural seedbank. Proc. South. Weed Sci. Soc. 59: 177.Google Scholar
Keeley, P. E., Carter, C. H., and Thullen, R. M. 1987. Influence of planting date on growth of Palmer amaranth (Amaranthus palmeri). Weed Sci. 35: 199–204.Google Scholar
Keivani, M., Ramezanpour, S. S., Soltanloo, H., Choukan, R., Naghavi, M., and Ranjbar, M. 2010. Genetic diversity assessment of alfalfa (Medicago sativa L.) populations using AFLP markers. Aust. J. Crop Sci. 4: 491–497.Google Scholar
Klingaman, T. E. and Oliver, L. R. 1994. Palmer amaranth (Amaranthus palmeri) interference in soybeans (Glycine max). Weed Sci. 42: 523–527.Google Scholar
Lima, M. L. A., Garcia, A. A. F., Oliveira, K. M., Matsuoka, S., Arizono, H., de Souza, C. L. Jr., and de Souza, A. P. 2002. Analysis of genetic similarity detected by AFLP and coefficient of parentage among genotypes of sugar cane (Saccharum spp.). Theor. Appl. Genet. 104: 30–38.Google Scholar
Mangolin, C. A., de Oliveira, R. S. Jr., and Machado, M. F. P. S. 2012. Genetic diversity in weeds. Pages 223–248 in Fernandez, R. A., ed. Herbicides-Environmental Impact Studies and Management Approaches. Rijeka, Croatia: InTech Europe, Available online: http://www.intechopen.com/books/herbicides-environmental-impact-studies-and-management-approaches/genetic-diversity-and-structure-of-weed-plant-populations.Google Scholar
Martos, V., Royo, C., Rharrabti, Y., and Garcia del Moral, L. F. 2005. Using AFLPs to determine phylogenetic relationships and genetic erosion in durum wheat cultivars released in Italy and Spain throughout the 20th century. Field Crops Res. 91: 107–116.Google Scholar
McRoberts, N., Sinclair, W., McPherson, A., Franke, A. C., Saharan, R. P., Malik, R. K., Singh, S., and Marshall, G. 2005. An assessment of genetic diversity within and between populations of Phalaris minor using ISSR markers. Weed Res. 45: 431–439.Google Scholar
Milla, S. R., Isleib, T. G., and Stalker, H. T. 2005. Taxonomic relationships among Arachis species as revealed by AFLP markers. Genome. 48: 1–11.Google Scholar
Nei, M. and Li, W. H. 1976. The transient distribution of allele frequencies under mutation pressure. Genet. Res. Camb. 28: 205–214.Google Scholar
Nissen, S. J., Masters, R. A., Lee, D. J., and Rowe, M. L. 1995. DNA-based marker systems to determine genetic diversity of weedy species and their application to biocontrol. Weed Sci. 43: 504–513.Google Scholar
Norsworthy, J. K., Oliveira, M. J., Jha, P., Malik, M., Buckelew, J. K., Jennings, K. M., and Monks, D. W. 2008. Palmer amaranth and large crabgrass growth with plasticulture-grown Capsicum annuum . Weed Technol. 22: 296–302.Google Scholar
Pester, A. P., Ward, S. M., Fenwick, A. L., Westra, P., and Nissen, S. J. 2003. Genetic diversity of jointed goatgrass (Aegilops cylindrica) determined with RAPD and AFLP markers. Weed Sci. 51: 287–293.Google Scholar
Powell, W., Morgante, M., and Andre, C. 1996. The comparison of RFLP, RPD, AFLP and SSR (microsatellite) markers for germplasm analysis. Mol. Breed. 2: 225–338.Google Scholar
Price, S. C., Allard, R. W., Hill, J. E., and Naylor, J. 1985. Associations between discrete genetic loci and genetic variability for herbicide reaction in plant populations. Weed Sci. 33: 650–653.Google Scholar
Radosevich, S., Holt, J., and Ghersa, C. 2007. Ecology of Weeds: Relationship to Agriculture and Natural Resource Management. 3rd ed. Hoboken, NJ: John Wiley and Sons. 150 p.Google Scholar
Ranade, S. A., Kumar, A., Goswami, M., Farooqui, N., and Sane, P. V. 1997. Genome analysis of amaranths: determination of inter- and intraspecies variations. J. Biosci. 22: 457–464.Google Scholar
Ray, T. and Roy, S. C. 2009. Genetic diversity of Amaranthus species from Indo-gangetic plains revealed by RAPD analysis leading to the development of ecotype-specific SCAR marker. J. Hered. 100: 338–347.Google Scholar
Rohlf, F. J. 2000. NTSYS-PC: numerical taxonomy and multivariate analysis system, version 2.2. Setauket, NY: Exeter Software.Google Scholar
Rold'an-Ruiz, I., Dendauw, J., Van Bockstaele, E., Depicker, A., and De Loose, M. 2000. AFLP markers reveal high polymorphic rates in ryegrasses (Lolium spp.). Mol. Breed. 6: 125–134.Google Scholar
Russell, J. R., Fuller, J. D., and Macaulay, M. 1997. Direct comparison of levels of genetic variation among barley accessions detected by RFLPs, AFLPs, SSRs, and RAPDs. Theor. App. Genet. 95: 714–722.Google Scholar
Saitou, M. and Nei, N. 1987. The neighbor joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4: 406–425.Google Scholar
Schneider, S., Roessli, D., and Excoffier, L. 2002. ARLEQUIN version 2.001: a software for population genetics data analysis. Geneva, Switzerland: Genetics and Biometry Laboratory, University of Geneva, Switzerland, Available at: http://lgb.unige.ch/arlequin/software.Google Scholar
Sharma, S. K., Knox, M. R., and Ellis, T. H. N. 1996. AFLP analysis of diversity and phylogeny of lens and its comparison with RAPD analysis. Theor. App. Gen. 93: 751–758.Google Scholar
Slotta, T. A. B. 2008. What we know about weeds: insights form genetic markers. Weed Sci. 56: 322–326.Google Scholar
Smith, D. T., Baker, R. V., and Steele, G. L. 2000. Palmer amaranth (Amaranthus palmeri) impacts on yield, harvesting, and ginning in dryland cotton (Gossypium hirsutum). Weed Technol. 14: 122–126.Google Scholar
Sosnoskie, L. M., Webster, T. M., Kichler, J. M., Macrae, A. W., and Culpepper, A. S. 2007. An estimation of pollen flight time and dispersal distance for glyphosate-resistant Palmer amaranth (Amaranthus palmeri). Proc. South. Weed Sci. Soc. 60: 229.Google Scholar
Sterling, T. M., Thompson, D. C., and Abbott, L. B. 2004. Implications of invasive plant variation for weed management. Weed Technol. 18: 1319–1324.Google Scholar
Tabacchi, M., Mantegazza, R., Spada, A., and Ferrero, A. 2006. Morphological traits and molecular markers for classification of Echinochloa species from Italian rice fields. Weed Sci. 54: 1086–1093.Google Scholar
Ulloa, O., Ortega, F., and Campos, H. 2003. Analysis of genetic diversity in red clover (Trifolium pretense L.) breeding populations as revealed by RAPD genetic markers. Genome. 46: 529–535.Google Scholar
Varshney, R. K., Chabane, K., Hendre, P. S., Aggarwal, R. K., and Graner, A. 2007. Comparative assessment of EST-SSR, EST-SNP and AFLP markers for evaluation of genetic diversity and conservation of genetic resources using wild, cultivated, and elite barleys. Plant Sci. 173: 638–649.Google Scholar
Vekemans, X., Beauwens, T., Lemaire, M., and Ruiz, I. R. 2002. Data from amplified fragment length polymorphism (AFLP) markers show indication of size homoplasy and of a relationship between degree of homoplasy and fragment size. Mol. Ecol. 11: 139–151.Google Scholar
Vos, P., Hogers, R., Bleeker, M., Reijans, M., van de Lee, T., Hornes, M., Frijters, A., Pot, J., Peleman, J., Kuiper, M., and Zabeau, M. 1995. AFLP: a new technique for DNA fingerprinting. Nuc. Acids Res. 23: 4407–4414.Google Scholar
Warwick, S. I. 1991. Herbicide resistance in weedy plants: physiology and population biology. Annu. Rev. Ecol. Syst. 22: 95–114.Google Scholar
Wassom, P. J. and Tranel, J. J. 2005. Amplified fragment length polymorphism-based genetic relationships among weedy Amaranthus species. J. Hered. 96: 410–416.Google Scholar
Webster, T. M. 2004. Weed survey—southern states. Proc. South. Weed Sci. Soc. 57: 404–426.Google Scholar
Webster, T. M. 2005. Weed survey—southern states. Proc. South. Weed Sci. Soc. 58: 291–306.Google Scholar
Webster, T. M. and Coble, H. D. 1997. Changes in the weed species composition of the southern United States: 1974–1995. Weed Technol. 11: 308–317.Google Scholar