Plant Diversity     2017 39 (05):  287-293    ISSN: 2096-2703:  CN: 53-1233

Identification of massive molecular markers in Echinochloa phyllopogon using a restriction-site associated DNA approach
Guoqi Chena,b, Wei Zhanga,b, Jiapeng Fanga,b, Liyao Donga,b
a College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China;
b Key Laboratory of Integrated Pest Management on Crops in East China(Nanjing Agricultural University), Ministry of Agriculture, Nanjing 210095, China
Received 2017-02-22  Revised 2017-08-28  Online 2017-10-25
Reference  Baird, N.A., Etter, P.D., Atwood, T.S., et al., 2008. Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS One 3, e3376.
Barchi, L., Lanteri, S., Portis, E., et al., 2011. Identification of SNP and SSR markers in eggplant using RAD tag sequencing. BMC Genomics 12.
Catchen, J.M., Amores, A., Hohenlohe, P., et al., 2011. Stacks: building and genotyping loci De Novo from short-read sequences. G3 Genes Genomes Genet. 1, 171-182.
Danquah, E.Y., Hanley, S.J., Brookes, R.C., et al., 2002. Isolation and characterization of microsatellites in Echinochloa (L.) Beauv. spp. Mol. Ecol. Notes 2, 54-56.
Flora of China, 2015. Available from:
Gupta, S.K., Baek, J., Carrasquilla-Garcia, N., et al., 2015. Genome-wide polymorphism detection in peanut using next-generation restriction-site-associated DNA (RAD) sequencing. Mol. Breed. 35.
Heap, I., 2015. The International Survey of Herbicide Resistant Weeds, 2015.Available from:
Holm, L.G., Pancho, J.V., Herberger, J.P., 1979. A Geographical Atlas of World Weeds.John Wiley and Sons, New York.
Kaya, H.B., Demirci, M., Tanyolac, B., 2014. Genetic structure and diversity analysis revealed by AFLP on different Echinochloa spp. from northwest Turkey. Plant Syst. Evol. 300, 1337-1347.
Kruglyak, L., 1997. The use of a genetic map of biallelic markers in linkage studies.Nat. Genet. 17, 21-24.
Lee, J., Park, K.W., Lee, I.Y., et al., 2015. Simple sequence repeat analysis of genetic diversity among acetyl-CoA carboxylase inhibitor-resistant and -susceptible Echinochloa crus-galli and E. oryzicola populations in Korea. Weed Res. 55, 90-100.
Miller, M.R., Dunham, J.P., Amores, A., et al., 2007. Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers. Genome Res. 17, 240-248.
Meirmans, P.G., 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.
Nozawa, S., Takahashi, M., Nakai, H., et al., 2006. Difference in SSR variations between japanese barnyard millet (Echinochloa esculenta) and its wild relative. E.crus-galli. Breed. Sci. 56, 335-340.
Okada, M., Hanson, B.D., Hembree, K.J., et al., 2013. Evolution and spread of glyphosate resistance in Conyza canadensis in California. Evol. Appl. 6, 761-777.
Orjuela, J., Garavito, A., Bouniol, M., et al., 2010. A universal core genetic map for rice. Theor. Appl. Genet. 120, 563-572.
Osuna, M.D., Okada, M., Ahmad, R., et al., 2011. Genetic diversity and spread of thiobencarb resistant early watergrass (Echinochloa oryzoides) in California.Weed Sci. 59, 195-201.
Peakall, R., Smouse, P.E., 2012. GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and researchdan update. Bioinformatics 28, 2537-2539.
Raats, D., Frenkel, Z., Krugman, T., et al., 2013. The physical map of wheat chromosome 1BS provides insights into its gene space organization and evolution.Genome Biol. 14, 19.
Rao, A.N., Johnson, D.E., Sivaprasad, B., et al., 2007. Weed management in directseeded rice. In: Donald, L.S. (Ed.), Advances in Agronomy. Academic Press, pp. 153-255.
Šmarda, P., Bures, P., Horova, L., et al., 2014. Ecological and evolutionary signi ficance of genomic GC content diversity in monocots. Proc. Natl. Acad. Sci. U. S. A. 111, E4096-E4102.
Sun, J.T., Wang, M.M., Zhang, Y.K., et al., 2015. Evidence for high dispersal ability and mito-nuclear discordance in the small brown planthopper, Laodelphax striatellus. Sci. Rep. 5, 8045.
Tabacchi, M., Mantegazza, R., Spada, A., et al., 2006. Morphological traits and molecular markers for classification of Echinochloa species from Italian rice fields.Weed Sci. 54, 1086-1093.
Talukder, Z.I., Gong, L., Hulke, B.S., et al., 2014. A high-density SNP map of sunflower derived from RAD-sequencing facilitating fine-mapping of the rust resistance gene R12. PLoS One 9, e98628.
Teixeira, H., Rodríguez-Echeverría, S., Nabais, C., 2014. Genetic diversity and differentiation of Juniperus thurifera in Spain and Morocco as determined by SSR.PLoS One 9, e88996.
Temnykh, S., DeClerck, G., Lukashova, A., et al., 2001. Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations, and genetic marker potential. Genome Res. 11, 1441-1452.
Vandepitte, K., Honnay, O., Mergeay, J., et al., 2013. SNP discovery using Paired-End RAD-tag sequencing on pooled genomic DNA of Sisymbrium austriacum (Brassicaceae). Mol. Ecol. Resour. 13, 269-275.
Vidotto, F., Tesio, F., Tabacchi, M., et al., 2007. Herbicide sensitivity of Echinochloa spp. accessions in Italian rice fields. Crop Prot. 26, 285-293.
Wang, Y., Yang, C., Jin, Q.J., et al., 2015. Genome-wide distribution comparative and composition analysis of the SSRs in Poaceae. BMC Genet. 16, 8.
Yamasue, Y., 2001. Strategy of Echinochloa oryzicola Vasing. for survival in flooded rice. Weed Biol. Manag. 1, 28-36.
Zhang, Q., Ma, B., Li, H., et al., 2012. Identification, characterization, and utilization of genome-wide simple sequence repeats to identify a QTL for acidity in apple.BMC Genomics 13.
Zhang, Y., Zalapa, J., Jakubowski, A., et al., 2011. Post-glacial evolution of Panicum virgatum: centers of diversity and gene pools revealed by SSR markers and cpDNA sequences. Genetica 139, 933-948.

Corresponding author: Liyao Dong,E-mail