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http://dx.doi.org/10.7744/kjoas.20170042

Digestion efficiency differences of restriction enzymes frequently used for genotype-by-sequencing technology  

Chung, Yong Suk (Department of Crop Science, College of Life Sciences, Chungnam National University)
Jun, Taehwan (Department of Crop Science, Pusan National University)
Kim, Changsoo (Department of Crop Science, College of Life Sciences, Chungnam National University)
Publication Information
Korean Journal of Agricultural Science / v.44, no.3, 2017 , pp. 318-324 More about this Journal
Abstract
With the development of next-generation sequencing (NGS), a cutting-edge technology, genotype-by-sequencing (GBS) became available at a low cost per sample. GBS makes it possible to customize the process of library preparation to obtain high-quality single nucleotide polymorphisms (SNPs) in the most efficient way. However, a GBS library is hard to construct due to fine-tuning of concentration of each reagent and set-up. The major reason for this is the presence of undigested genomic DNA (gDNA) owing to the efficiency of different restriction enzymes for different species with unknown reasons. Therefore, this proof-concept study is to demonstrate the unpredictable patterns of enzyme digestion from various plants in order to make the reader aware of the caution needed when choosing restriction enzymes for their GBS library preparations. Indeed, no pattern was found for the digestibility of gDNA samples and restriction enzymes in the current study. We suggest that more data should be accumulated on this matter to help researchers who want to apply GBS technologies in a variety of genetic approaches.
Keywords
dicot; monocot; next-generation sequencing; plant genomic DNA; restriction digestion;
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1 Guillemaut P, Maréchal-Drouard L. 1992. Isolation of plant DNA: A fast, inexpensive, and reliable method. Plant Molecular Biology Reporter 10:60-5.   DOI
2 Arabidopsis Genome Initiative. 2000. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796-815.   DOI
3 Comb M, Goodman HM. 1990. CpG methylation inhibits proenkephalin gene expression and binding of the transcription factor AP-2. Nucleic Acids Research 18:3975-3982.   DOI
4 Davey JW, Hohenlohe PA, Etter PD, Boone JQ, Catchen JM, Blaxter ML. 2011. Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nature Reviews Genetics 12:499-510.   DOI
5 Doyle J, Doyle JL. 1987. Genomic plant DNA preparation from fresh tissue-CTAB method. Phytochemical Bulletin 19:11-5.
6 Elshire RJ, Glaubitz JC, Sun Q, Poland JA, Kawamoto K, Buckler ES, Mitchell SE. 2011. A robust, simple genotypingby-sequencing (GBS) approach for high diversity species. PloS ONE 6:e19379.   DOI
7 Gore M, Bradbury P, Hogers R, Kirst M, Verstege E, van Oeveren J, Peleman J, Buckler E, van Eijk M. 2007. Evaluation of target preparation methods for single-feature polymorphism detection in large complex plant genomes. Crop Science 47:S-135-S-148.
8 Gore MA, Chia J-M, Elshire RJ, Sun Q, Ersoz ES, Hurwitz BL, Peiffer JA, McMullen MD, Grills GS, Ross-Ibarra J. 2009. A first-generation haplotype map of maize. Science 326:1115-1117.   DOI
9 He J, Zhao X, Laroche A, Lu ZX, Liu H, Li Z. 2014. Genotyping-by-sequencing (GBS), an ultimate marker-assisted selection (MAS) tool to accelerate plant breeding. Frontiers in Plant Science 5:484.
10 Honeycutt RJ, Sobral BW, Keim P, Irvine JE. 1992. A rapid DNA extraction method for sugarcane and its relatives. Plant Molecular Biology Reporter 10:66-72.   DOI
11 Kim C, Guo H, Kong W, Chandnani R, Shuang L-S, Paterson AH. 2016. Application of genotyping by sequencing technology to a variety of crop breeding programs. Plant Science 242:14-22.   DOI
12 Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, Gundlach H, Haberer G, Hellsten U, Mitros T, Poliakov A, Schmutz J, Spannagl M, Tang H, Wang X, Wicker T, Bharti AK, Chapman J, Feltus FA, Gowik U, Grigoriev IV, Lyons E, Maher CA, Martis M, Narechania A, Otillar RP, Penning BW, Salamov AA, Wang Y, Zhang L, Carpita NC, Freeling M, Gingle AR, Hash CT, Keller B, Klein P, Kresovich S, McCann MC, Ming R, Peterson DG, Rahman M, Ware D, Westhoff P, Mayers KF, Messing J, Rokhsar DS. 2009. The Sorghum bicolor genome and the diversification of grasses. Nature 457:551-556.   DOI
13 Poland JA, Rife TW. 2012. Genotyping-by-sequencing for plant breeding and genetics. Plant Genome 5:92-102.   DOI
14 Zhu H, Qu F, Zhu, LH. 1993. Isolation of genomic DNAs from plants, fungi and bacteria using benzyl chloride. Nucleic Acids Research 21:5279.   DOI
15 Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S, Liang C, Zhang J, Fulton L, Graves TA, Minx P, Reily AD, Courtney L, Kruchowski SS, Tomlinson C, Strong C, Delehaunty K, Fronick C, Courtney B, Rock SM, Belter E, Du F, Kim K, Abbott RM, Cotton M, Levy A, Marchetto P, Ochoa K, Jackson SM, Gillam B, Chen W, Yan L, Higginbotham J, Cardenas M, Waligorski J, Applebaum E, Phelps L, Falcone J, Kanchi K, Thane T, Scimone A, Thane N, Henke J, Wang T, Ruppert J, Shah N, Rotter K, Hodges J, Ingenthron E, Cordes M, Kohlberg S, Sgro J, Delgado B, Mead K, Chinwalla A, Leonard S, Crouse K, Collura K, Kudrna D, Currie J, He R, Angelova A, Rajasekar S, Mueller T, Lomeli R, Scara G, Ko A, Delaney K, Wissotski M, Lopez G, Campos D, Braidotti M, Ashley E, Golser W, Kim H, Lee S, Lin J, Dujmic Z, Kim W, Talag J, Zuccolo A, Fan C, Sebastian A, Kramer M, Spiegel L, Nascimento L, Zutavern T, Miller B, Ambroise C, Muller S, Spooner W, Narechania A, Ren L, Wei S, Kumari S, Faga B, Levy MJ, McMahan L, Van Buren P, Vaughn M, Ying K, Yeh CT, Emrich SJ, Jia Y, Kalyanaraman A, Hsia AP, Barbazuk WB, Baucom RS, Brutnell TP, Carpita NC, Chaparro C, Chia JM, Deragon JM, Estill JC, Fu Y, Jeddeloh JA, Han Y, Lee H, Li P, Lisch DR, Liu S, Liu Z, Nagel DH, McCann MC, SanMiguel P, Myers AM, Nettleton D, Nguyen J, Penning BW, Ponnala L, Schneider KL, Schwartz DC, Sharma A, Soderlund C, Springer NM, Sun Q, Wang H, Waterman M, Westerman R, Wolfgruber TK, Yang L, Yu Y, Zhang L, Zhou S, Zhu Q, Bennetzen JL, Dawe RK, Jiang J, Jiang N, Presting GG, Wessler SR, Aluru S, Martienssen RA, Clifton SW, McCombie WR, Wing RA, Wilson RK. 2009. The B73 maize genome: Complexity, diversity, and dynamics. Science 326:1112-1115.   DOI
16 Susan JC, Harrison J, Paul CL, Frommer M. 1994. High sensitivity mapping of methylated cytosines. Nucleic Acids Research 22: 2990-2997.   DOI