Article | . Vol. 8, Issue. 1
Development of Cross-specific Microsatellite Markers for Echinochloa spp. (Poaceae)



National Institute of Agricultural Sciences, Rural Development Administration, Wanju 55365, Korea1




.. 21:29


PDF XML




Echinochloa spp. is one of the most problematic weeds, especially in rice fields. Therefore, most of the studies on this genus have been focused on chemical control. Its genetic diversity using molecular markers was not widely studied because of a few markers available. Microsatellite markers were developed in this study to evaluate the genetic diversity of a cross-specific troublesome weed Echinochloa species (Poaceae). Illumina sequencing identified a total of 44,257 di-/tri-nucleotide repeat motifs. Finally, thirteen microsatellite markers were identified for Echinochloa crus-galli. All markers were polymorphic and cross amplified in E. oryzicola. The average number of alleles per locus was 8.0 and polymorphism information content was 0.611. Observed and expected heterozygosity ranged from 0.00 to 0.98 and from 0.06 to 0.86, respectively. The 13 polymorphic markers identified in this study will be useful for assessing the genetic diversity of E. crus-galli along with E. oryzicola and for predicting the dispersal pattern of these weeds in agricultural fields.



1.  Chen, G., Zhang, W., Fang, J. and Dong, L. 2017. Restriction site-associated DNA sequencing allows for the rapid identification of simple sequence repeat markers in . Weed Biol. Manage. 17(2):68-76.  

2.  Clayton, W.D. and Renvoize, S.A. 1999. Genera graminum, grasses of the world. edited by Coode, M.J.E. Vol. XIII. Royal Botanic Gardens, London, UK. 280-281.  

3.  Compeau, P.E.C., Pevzner, P.A. and Tesler, G. 2011. How to apply de Bruijn graphs to genome assembly. Nat. Biotech. 29(11):987-991.  

4.  Danquah, E.Y., Hanley, S.J., Brookes, R.C., Aldam, C. and Karp, A. 2002. Isolation and characterization of microsatellites in (L.) Beauv. spp. Mol. Ecol. Notes 2(1):54-56.  

5.  Heap, I. 2018. The international survey of herbicide resistant weeds. http//:www.weedscience.org  

6.  Lee, E.J., Nah, G., Yook, M.J., Lim, S.H., Park, T.S., et al. 2016. Phylogentic relationship of species based on simple sequence repeat and phenotypic marker analyses. Weed Sci. 64:441-454.  

7.  Lee, J., Kim, C.S. and Lee, I.Y. 2013. Identification of oryzicola (Vasinger) Vasinger and E. oryzoides (Ard.) Fritsch in Korea. Kor. J. Pla. Tax. 43(1):56-62. (In Korean)  

8.  Lee, J., Kim, C.S. and Lee, I.Y. 2014. Taxonomic review of the genus in Korea (II): Inferred from simple sequence repeats. Weed Turf. Sci. 3(3):190-195.   

9.  Lee, J., Park, K.W., Lee, I.Y., Kim, C.S., Kown, O.D., et al. 2015. Simple sequence repeat analysis of genetic diversity among Acetyl-CoA carboxylase inhibitor-resistant and -susceptible and populations in Korea. Weed Res. 55(1):90-100.   

10. Li, R., Zhu, H., Ruan, J., Qian, W., Fang, X., et al. 2010. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res. 20(2):265-272.   

11.  Liu, K. and Muse, S.V. 2005. PowerMarker: Integrated analysis environment for genetic marker data. Bioinformatics 21(9):2128-2129.  

12.  Lopez-Martinez, N., Salva, A.P., Finch, R.P., Marshall, G. and Prado, R.D. 1999. Molecular markers indicate intraspecific variation in the control of spp. with quinclorac. Weed Sci. 47(3):310-315.  

13.  Moon, B.C., Won, J.G., Kim, Y.L., Kim, S.W., Lee, I.Y., et al. 2011. Prediction of rice yield and economic.  

14. Nie, X.J., Liu, P.X., Deng, P.C., Lu, Y.Z., Biradar, S.S., et al. 2014. Large-scale identification of microsatellites for a major invasive weed, Ageratina adenophora, using the Illumina sequencing technology. Weed Res. 54(2):133-139.  

15.  Peakall, R. and Smouse, P. 2006. GENALEX 6: Genetic analysis in excel. Population genetic software for teaching and research. Mol. Ecol. Notes 6(1):288-295.  

16.  Pineda-Martos, R., Velasco, L. and Pérez-Vich, B. 2014. Identification, characterisation and discriminatory power of microsatellite markers in the parasitic weed Orobanche cumana . Weed Res. 54(2):120-132.   

17.  Rozen, S. and Skaletsky, H. 2000. Primer3 on the WWW for general users and for biologist programmers. In Krawetz, S. and Misener S. (Eds.). Bioinformatics methods and protocols: Methods in molecular biology. pp. 365-386. Humana Press, Totowa, USA.  

18.  Rutledge, J., Talbert, R.E. and Sneller, C.H. 2000. RAPD analysis of genetic variation among propanilresistant and -susceptible populations in Arkansas. Weed Sci. 48(6):669-674.  

19. Warwick, S.I. and Weaver, S.E. 1980. Atrazine resistance in Amaranthus retroflexus (redroot pigweed) and Amaranthus powellii (green pigweed) from southern Ontario. Can. J. Plant Sci. 60(4):1485-1488.  

20.  Wright, S.I. and Gaut, B.S. 2005. Molecular population genetics and the search for adaptive evolution in plants. Mol. Biol. Evol. 22(3):506-519.  

21.  Yu, J.N., Won, C., Jun, J., Lim, Y. and Kwak, M. 2011. Fast and cost-effective mining of microsatellite  



online submission
Sub Menu
Sub Banner
Sub Banner
Sub Menu
Sub Banner
Sub Banner
Sub Banner
Sub Banner
Sub Menu
Sub Menu