A Survey of Genetic Diversity of the Weedy Species Ipomoea lacunosa L. in the USA Mid-South

Nilda R. Burgos, Daniel O. Stephenson, Hesham A. Agrama, Lawrence R. Oliver, Jason A. Bond

.

DOI: 10.4236/ajps.2011.23045                

Abstract

Morningglories (Ipomoea spp.) are among the most troublesome weedy species in agroecological environments. Ipomoea lacunosa is one of the most prevalent of these species. Localized adaptations resulted in the evolution of several I. lacunosa ecotypes in North America, which could potentially impact its response to crop management practices. To evaluate the genetic diversity and population structure of I. lacunosa populations, we amplified inter-simple sequence repeats loci by polymerase chain reaction (ISSR-PCR) of 64 accessions using 14 ISSR primers for Ipomoea. Of these, 64 polymorphic fragments were scored. Analysis of Nei’s genetic distance (GD) values placed the accessions into four genotypic clusters, two of which were composed primarily of accessions from Arkansas and Mississippi with GD between clusters of 0.318. The overall GD was 0.238, indicating a narrow genetic base. Population structure analysis determined three ancestral subgroups, with the majority of Arkansas and Mississippi accessions separated into two subgroups. The existence of various genotypes and ecotypes of I. lacunosa demonstrates the evolutionary diversification of this weedy species as it adapts to new colonized environments and agricultural activities.

Keywords

DNA Fingerprinting, Genetic Diversity, Ipomoea, ISSR, Morningglory Species, Morningglory Genotypes, Population Structure

Conflicts of Interest

The authors declare no conflicts of interest.

References

[1]	C. D. Elmore, H. R. Hurst and D. F. Austin, “Biology and Control of Morningglories (Ipomoea spp.),” Reviews in Weed Science, Vol. 5, 1990, pp. 83-114.
[2]	J. A. McDonald and T. J. Mabry, “Phylogenetic Systematic of New World Ipomoea (Convolvulaceae) Based on Chloroplast DNA Restriction Site Variation,” Plant Systematic Evolution, Vol. 180, 1992, pp. 243-259.
[3]	D. F. Austin and Z. Huáman, “A Synopsis of the Ipomoea (Convolvulaceae) in the Americas,” Taxon, Vol. 45, 1996, pp. 3-38.
[4]	M. A. Barker, L. Thompson Jr, and F. M. Godley, “Control of Annual Morningglories (Ipomoea spp.) in Soybeans (Glycine max),” Weed Science, Vol. 32, 1984, pp. 813-818.
[5]	C. D. Elmore, J. B. Wiseman and S. McDaniel, “Morningglory Survey of Cotton and Soybean Fields in the Mississippi Delta: 1981,” Proceedings Southern Weed Science Society, Vol. 35, 1982, pp. 319-328.
[6]	M. L. Fernald, “Gray’s Manual of Botany,” 8th Edition (Centennial), American Book Company, New York, 1950.
[7]	A. E. Radford, H. E. Ahles and C. R. Bell, “Manual of the Vascular Flora of the Carolinas,” The University of North Carolina Press, Chapel Hill, 1968.
[8]	T. M. Webster, “Weed Survey—Southern States: Broadleaf Crops Subsection,” Annual Meeting Abstracts, Southern Weed Science Society, Champaign, 2005.
[9]	T. M. Webster, “Weed Survey—Southern States: Vegetables, Fruits, and Nut Crops,” Annual Meeting Abstracts, Southern Weed Science Society, Champaign, 2006.
[10]	O. W. Howe III and L. R. Oliver, “Influence of Soybean (Glycine max) Row Spacing on Pitted Morningglory Interference,” Weed Science, Vol. 35, 1987, pp. 185-193.
[11]	C. D. Elmore, “Weed Survey—Southern States,” Southern Weed Science Society Report, Vol. 37, 1984, pp. 192-198.
[12]	D. O. Stephenson IV, L. R. Oliver, N. R. Burgos and E. E. Gbur Jr, “Identification and Characterization of Pitted Morningglory (Ipomoea lacunosa) Ecotypes,” Weed Science, Vol. 54, No.1, 2006, pp. 78-86. doi:10.1614/WS-04-205R.1
[13]	C. T. Bryson, K. N. Reddy and I. C. Burke, “Morphological Comparison of Morningglory (Ipomoea and Jacquemontia spp.) Populations from the Southeastern United States,” Weed Science, Vol. 56, No. 5, 2008, pp. 692-698. doi:10.1614/WS-07-198.1
[14]	C. D. Elmore, “Mode of Reproduction and Inheritance of Leaf Shape in Ipomoea hederacea,” Weed Science, Vol. 34, 1986, pp. 391-395.
[15]	M. Jasieniuk and B. D. Maxwell, “Plant Diversity: New Insights from Molecular Biology and Genomics Technologies,” Weed Science, Vol. 49, No. 2, 2001, pp. 257-265. doi:10.1614/0043-1745(2001)049[0257:PDNIFM]2.0.CO;2
[16]	L. Dekker, “Weed Diversity and Weed Management,” Weed Science, Vol. 45, 1997, pp. 357-363.
[17]	E. P. Odum, “Fundamentals in Ecology,” 3rd Edition, W. B. Saunders Co., Philadelphia, 1971.
[18]	I. C. Burke, K. N. Reddy and C. T. Bryson, “Pitted and Hybrid Morningglory Accessions Have Variable Tolerance to Glyphosate,” Weed Technology, Vol. 23, No. 4, 2009, pp. 592-598. doi:10.1614/WT-09-028.1
[19]	J. J. Doyle and J. L. Doyle, “Isolation of Plant DNA from Fresh Tissue,” Focus, Vol. 1, 1990, pp. 13-15.
[20]	J. C. Huang and M. Sun, “Genetic Diversity and Relationships of Sweet Potato and Its Wild Relatives in Ipomoea series Batatas (Convolvulaceae) as Revealed by Inter-Simple Sequence Repeat (ISSR) and Restriction Analysis of Chloroplast DNA,” Theoretical and Applied Genetics, Vol. 100, No. 7, 2000, pp. 1050-1060. doi:10.1007/s001220051386
[21]	M. V. Katti, P. K. Ranjekar and V. S. Gupta, “Differential Distribution of Simple Sequence Repeats in Eukaryotic Genome Sequences,” Molecular Biology and Evolution, Vol. 18, 2001, pp. 1161-1167.
[22]	E. Zietkiewicz, A. Rafalski and D. Labuda, “Genomic Fingerprinting by Simple Sequence Repeat (SSR)-Anchored Polymerase Chain Reaction Amplification,” Genomics, Vol. 20, 1994, pp. 176-183.
[23]	B. Liu and J. F. Wendel, “Intersimple Sequence Repeat (ISSR) Polymorphisms as a Genetic Marker in Cotton,” Molecular Ecology Notes, Vol. 1, No. 3, 2001, pp. 205-208. doi:10.1046/j.1471-8278.2001.00073.x
[24]	M. Morgante and M. Olivieri, “PCR-Amplified Microsatellites as Markers in Plant Genetics,” Plant Journal, Vol. 3, 1993, pp. 175-182. doi:10.1111/j.1365-313X.1993.tb00020.x
[25]	P. C. O. Hanlon, R. Peakall and D. T. Briese, “A Review of New PCR-Based Genetic Markers and Their Utility to Weed Ecology,” Weed Research, Vol. 40, No. 3, 2000, pp. 239-254. doi:10.1046/j.1365-3180.2000.00191.x
[26]	M. Z. Galvan, B. Bornet, P. A. Balatti and M. Branchard, “Inter Simple Sequence Repeat (ISSR) Markers as a Tool for the Assessment of Both Genetic Diversity and Gene Pool Origin in Common Bean (Phaseolus vulgaris L.),” Euphytica, Vol. 123, 2003, pp. 297-301.
[27]	G. A. Lallemand and M. Bourgoin, “Fast and Reliable Strawberry Cultivar Identification Using Inter Simple Sequence Repeat (ISSR) Amplification,” Euphytica, Vol. 129, 2002, pp. 69-79.
[28]	B. J. Parsons, H. J. Newbury, M. T. Jackson and B. V. Ford-Lloyd, “Contrasting Genetic Diversity Relationships Are Revealed in Rice (Oryza sativa L.) Using Different Marker Types,” Molecular Breeding, Vol. 3, No. 2, 1997, pp. 115-125. doi:10.1023/A:1009635721319
[29]	M. Nei, “Genetic Distance between Populations,” American Naturalist, Vol. 106, 1972, pp. 283-292.
[30]	K. Liu and S. V. Muse, “PowerMarker: An Integrated Analysis Environment for Genetic Marker Analysis,” Bioinformatics, Vol. 21, 2005, pp. 2128-2129.
[31]	F. J. Rohl, “NTSYS-pc: Numerical Taxonomy System, v 2.21,” Exeter Publishing, Ltd., New York, 2008.
[32]	G. McVean, “A Genealogical Interpretation of Principal Components Analysis,” PLoS Genetics, Vol. 5, No. 10, 2009, p. e1000686. doi:10.1371/journal.pgen.1000686
[33]	J. K. Pritchard, M. Stephens and P. Donnelly, “Inference of population structure using multilocus genotype data,” Genetics, Vol. 155, 2000, 945-959.
[34]	D. Falush, M. Stephens and J. K. Pritchard, “Inference of Population Structure Using Multilocus Genotype Data: Linked Loci and Correlated Allele Frequencies,” Genetics, Vol. 164, 2003, pp. 1567-1587.
[35]	A. L. Price, N. J. Patterson, R. M. Plenge, M. E. Weinblatt, N. A. Shadick and D. Reich, “Principal Components Analysis Corrects for Stratification in Genome-Wide Association Studies,” Nature Genetics, Vol. 38, No. 8, 2006, pp. 904-909. doi:10.1038/ng1847
[36]	N. Patterson, A. L. Price, D. Reich, “Population Structure and Eigen Analysis,” PloS Genetics, Vol. 2, No. 12, 2006, p. e190. doi:10.1371/journal.pgen.0020190
[37]	H. A. Agrama and G. C. Eizenga, “Molecular Diversity and Genome-Wide Linkage Disequilibrium Pattern in Worldwide Rice and Its Wild Relatives,” Euphytica, Vol. 160, 2008, pp. 339-355.
[38]	H. A. Agrama, J. M. Yan, R. Fjellstrom and A. M. McClung, “Genetic Structure Associated with Diversity and Geographic Distribution in the USDA Rice World Collection,” Natural Science, Vol. 2, No. 4, 2010, pp. 247-291. doi:10.4236/ns.2010.24036
[39]	G. C. Eizenga, H. A. Agrama, F. N. Lee and Y. Jia, “Exploring Genetic Diversity and Potential Novel Disease Resistance Genes in a Collection of Rice Wild Relatives,” Genetic Resources and Crop Evolution, Vol. 56, No. 1, 2009, pp. 65-76. doi:10.1007/s10722-008-9345-7
[40]	D. R. Gealy, H. A. Agrama and G. Eizenga, “Exploring the Genetic and Spatial Structure of U.S. Weedy Red Rice (Oryza sativa) Accessions in Relation to Global Oryza spp.,” Weed Science, Vol. 57, No. 6, 2009, pp. 627-643. doi:10.1614/WS-09-018.1
[41]	V. K. Shivrain, N. R. Burgos, H. A. Agrama, A. Lawton-Rauh, B. LU, M. A. Sales, V. Boyett, D. R. Gealy and K. A. K. Moldenhauer, “Genetic Diversity of Weedy Rice (Oryza sativa L.) in Arkansas, USA,” Weed Research, Vol. 50, 2010, pp. 289-302.
[42]	J. Xie, H. A. Agrama, D. Kong, J. Zhuang, W. Yan, B. Hu and Z. Zhuang, “Genetic Diversity of Endangered Dongxiang Wild Rice (Oryza rufipogon),” Genetic Resources and Crop Evolution, Vol. 57, No. 4, 2010, pp. 597-609. doi:10.1007/s10722-009-9498-z
[43]	W. Yan, H. A. Agrama, M. Jia, R. Fjellstrom and A. M. McClung, “Geographic Description of Genetic Diversity and Genetic Relationships in the USDA Rice World Collection,” Crop Science, Vol. 50, No. 6, 2010, pp. 2406-2417. doi:10.2135/cropsci2010.02.0096
[44]	G. Evanno, S. Regnaut and J. Goudet, “Detecting the Number of Clusters of Individuals Using the Software STRUCTURE: A Simulation Study,” Molecular Ecology, Vol. 14, No. 8, 2005, pp. 2611-2620. doi:10.1111/j.1365-294X.2005.02553.x
[45]	L. Excoffer, G. Laval and S. Schneider, “Arlequin (Version 3.0): An Integrated Software Package for Population Genetics Data Analysis,” Evolutionary Bioinformatics Online, Vol. 1, 2005, pp. 47-50.
[46]	S. A. Senseman and L. R. Oliver, “Flowering Patterns, Seed Production, and Somatic Polymorphism of Three Weed Species,” Weed Science, Vol. 41, 1993, p. 418-425.
[47]	B. Tanyolac, “Inter-Simple Sequence Repeat (ISSR) and RAPD Variation Among Wild Barley Hordeum vulgare subsp. spontaneum) Populations from West Turkey,” Genetic Resources in Crop Evolution, Vol. 50, No. 6, 2003, pp. 611-614. doi:10.1023/A:1024412814757
[48]	S. P. Joshi, V. S. Gupta, R. K. Aggarwal, P. K. Ranjekar and D. S. Brar, “Genetic Diversity and Phylogenetic Relationship as Revealed by Inter-Simple Sequence Repeat (ISSR) Polymorphism in the Genus Oryza,” Theoretical and Applied Genetics, Vol. 100, No. 8, 2000, pp. 1311-1320. doi:10.1007/s001220051440
[49]	T. Nagaoka and Y. Ogihara, “Applicability of Inter-Simple Sequence Repeat Polymorphisms in Wheat for Use as DNA Markers in Comparison to RFLP and RAPD Markers,” Theoretical and Applied Genetics, Vol. 94, No. 5, 1997, pp. 597-602. doi:10.1007/s001220050456