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Plant Diversity 2017, 39(05) 287-293 DOI:   10.1016/j.pld.2017.08.004  ISSN: 2096-2703 CN: 53-1233

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Echinochloa phyllopogon
RAD sequencing

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


Echinochloa phyllopogon proliferation seriously threatens rice production worldwide. We combined a restriction-site associated DNA (RAD) approach with Illumina DNA sequencing for rapid and mass discovery of simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers for E. phyllopogon. RAD tags were generated from the genomic DNA of two E. phyllopogon plants, and sequenced to produce 5197.7 Mb and 5242.9 Mb high quality sequences, respectively. The GC content of E. phyllopogon was 45.8%, which is high for monocots. In total, 4710 putative SSRs were identified in 4132 contigs, which permitted the design of PCR primers for E. phyllopogon. Most repeat motifs among the SSRs identified were dinucleotide (>82%), and most of these SSRs were four motif-repeats (>75%). The most frequent motif was AT, accounting for 36.3%-37.2%, followed by AG and AC. In total, 78 putative polymorphic SSR loci were found. A total of 49,179 SNPs were discovered between the two samples of E. phyllopogon, 67.1% of which were transversions and 32.9% were transitions. We used eight SSRs to study the genetic diversity of four E. phyllopogon populations collected from rice fields in China and all eight loci tested were polymorphic.

Keywords Echinochloa phyllopogon   Polymorphic   RAD sequencing   SNP   SSR  
Received 2017-02-22 Revised 2017-08-28 Online:  
DOI: 10.1016/j.pld.2017.08.004
Fund:This research was supported by China Postdoctoral Science Foundation (2015M571763) and the Special Fund for Agroscientific Research in the Public Interest of China (201303022).We thank Kui Wu and Zhi-hui Yan (Nanjing Agricultural University,China) for providing helps on plant cultivation.Thanks are also due to the reviewers and editors for their helpful comments and English polish on earlier drafts of the manuscript.
Corresponding Authors: Liyao Dong,E-mail address:dly@njau.edu.cn
Email: dly@njau.edu.cn
About author:

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: www.efloras.org.
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: www.weedscience.org.
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.
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