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2018 Vol.36, Issue 1 Preview Page
Optimization of Genotyping-by-sequencing (GBS) in Chrysanthemums: Selecting Proper Restriction Enzymes for GBS Library Construction
Toan Khac Nguyen1
,
Jaewoong Yu2
,
Hyung-Won Choi1
,
Byung-Chun In3
,
Jin-Hee Lim1*
1Department of Bioindustry and Bioresource Engineering, Sejong University
2Applied Research Department, C&K genomics Inc.
3Department of Horticulture and Breeding, Andong National University
*교신저자. *Corresponding Author. 
28 February 2018. pp. 108-114
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Abstract

Chrysanthemum is one of the most popular ornamental flowers in Korea due to its great diversity of colors and forms. To understand this diversity and to efficiently breed chrysanthemum varieties, a genetic diversity assessment of Korean native chrysanthemum populations using molecular markers is required. Genotyping-by-sequencing (GBS) is a newly developed and widely used next generation sequencing (NGS) method based on the single nucleotide polymorphism (SNP) marker system. In this study, we tested three restriction enzyme combinations (ApeKI, ApeKI/MseI, and ApeKI/MspI) for GBS library construction using eight Korean native Chrysanthemum spp. accessions. Three libraries were constructed and sequenced on the Illumina NextSeq 500 platform and results were analyzed in the Stacks de novo GBS pipeline. Overall, the ApeKI/MseI combination showed the best library quality, highest number of tags, and SNP generation potential.

Keywords
de novo GBS
genetic diversity
SNP
Stacks
wild native chrysanthemum

References
1
Baird NA, Etter PD, Atwood TS, Currey MC, Shiver AL, Lewis ZA, Selker EU, Cresko WA, Johnson EA (2008) Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS ONE 3:e3376. doi:10.1371/journal.pone.0003376
2
Barow M, Meister A (2002) Lack of correlation between AT frequency and genome size in higher plants and the effect of nonrandomness of base sequences on dye binding. Cytometry 47:1-7. doi:10.1002/cyto.10030
3
Catchen JM, Amores A, Hohenlohe P, Cresko W, Postlethwait JH (2011) Stacks: building and genotyping loci de novo from short-read sequences. G3 (Bethesda) 1:171-182. doi:10.1534/g3.111.000240
4
Chong X, Zhang F, Wu Y, Yang X, Zhao N, Wang H, Guan Z, Fang W, Chen F (2016) A SNP-Enable assessment of genetic diversity, evolutionary relationships and the identification of candidate genes in chrysanthemum. Genome Biol Evol 8:3661-3671
5
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 Rev Gen 12:499-510. doi:10.1038/nrg3012
6
De Donato M, Peters SO, Mitchell SE, Hussain T, Imumorin IG (2013) Genotyping-by-sequencing (GBS): a novel, efficient and cost-effective genotyping method for cattle using next generation sequencing. PLoS ONE 8:e62137. doi:10.1371/journal.pone.0062137
7
Deschamps S, Llaca V, May GD (2012) Genotyping-by-sequencing in plants. Biology 1:460-483. doi:10.3390/biology1030460
8
Elshire RJ, Glaubitz JC, Sun Q, Poland JA, Kawamoto K, Buckler ES, Mitchell SE (2011) A Robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS ONE 6:e19379. doi:10.1371/journal.pone.0019379
9
Fu YB, Cheng B, Peterson GW (2014) Genetic diversity analysis of yellow mustard (Sinapis alba L.) germplasm based on genotyping by sequencing. Genet Resour Crop Evol 61:579-594. doi:10.1007/s10722-013-0058-1
10
Fu YB, Peterson GW, Dong YB (2016) Increasing genome sampling and improving SNP genotyping for genotyping-by-sequencing with new combinations of restriction enzymes. G3 (Bethesda) 6:845-856. doi:10.1534/g3.115.025775
11
Hattman S, Brooks JE, Masurekar M (1978) Sequence specificity of the P1 modification methylase (M.Eco P1) and the DNA methylase (M.Eco dam) controlled by the Escherichia coli dam gene. J Mol Biol 126:367-380. doi:10.1016/0022-2836(78)90046-3
12
He J, Zhao X, Laroche A, Lu ZX, Liu HK, Li Z (2014) Genotyping-by-sequencing (GBS), an ultimate marker-assisted selection (MAS) tool to accelerate plant breeding. Front Plant Sci 10.3389/fpls.2014.00484. doi:10.3389/fpls.2014.00484
13
Iwatsuki K, Takasi Y, David EB, Hideaki O (1997) Flora of Japan, 3b, Angiospermae-Dicotyledoneae: Sympetalae (b). Kodansha, Tokyo, Japan
14
Kagale S, Koh C, Clarke WE, Bollina V, Parkin IAP, Sharpe AG (2016) Analysis of genotyping-by-sequencing (GBS) data. Plant Bioinfor 1374:269-284. doi:10.1007/978-1-4939-3167-5_15
15
Kim H, Jebrail MJ, Sinha A, Bent ZW, Solberg OD, Williams KP (2013) A microfluidic DNA library preparation platform for Next-generation sequencing. PLoS ONE 8:e68988. doi:10.1371/journal.pone.0068988
16
Kim SJ, Lee CH, Kim J, Kim KS (2014) Phylogenetic analysis of Korean native Chrysanthemum species based on morphological characteristics. Sci Hortic175:278-289. doi:10.1016/j.scienta.2014.06.018
17
Luo C, Chen D, Cheng X, Zhao H, Huang C (2016) Genome size estimations in Chrysanthemum and correlations with molecular phylogenies. Genet Res Crop Evol 64:1451-1463. doi:10.1007/s10722-016-0448-2
18
Liu L, Hu N, Wang B, Chen M, Wang J, Tian Z, He Y, Lin D (2011) A brief utilization report on the Illumina HiSeq 2000 sequencer. Mycology 2:169-191
19
May MS, Hattman S (1975) Analysis of bacteriophage deoxyribonucleic acid sequences methylated by host- and R-factor-controlled enzymes. J Bacteriol 123:768-770
20
Poland JA, Rife TW (2012) Genotyping-by-Sequencing for Plant Breeding and Genetics. Plant Genome 5:92-102. doi:10.3835/plantgenome2012.05.0005
21
Rabbi I, Hamblin M, Gedil M, Kulakow P, Ferguson M, Ikpan AS, Ly D, Jannink DL (2014) Genetic mapping using genotyping-by-sequencing in the clonally propagated Cassava. Crop Sci 54:1384-1396. doi:10.2135/cropsci2013.07.0482
22
Scheben A, Batley J, Edwards D (2016) Genotyping by sequencing approaches to characterise crop genomes: choosing the right tool for the right application. Plant Biotechnol J 15:149-161. doi:10.1111/pbi.12645
23
Vallès J, Canela MÁ, Garcia S, Hidalgo O, Pellicer J, Sánchez-Jiménez I, Siljak-Yakovlev S, Vitales D, Garnatje T (2013) Genome size variation and evolution in the family Asteraceae. Caryologia 66:221-235. doi:10.1080/00087114.2013.829690
24
van Orsouw NJ, Hogers RCJ, Janssen A, Yalcin F, Snoeijers S, Verstege E, Schneiders H, van der Poel H, van Oeveren J, et al (2007) Complexity reduction of polymorphic sequences (CRoPSTM): A novel approach for large-scale polymorphism discovery in complex genomes. PLoS ONE 2:e1172. doi:10.1371/journal.pone.0001172
25
Wang H, Jiang J, Chen S, Qi X, Peng H, Li P, Song A, Guan Z, Fang W, et al (2013) Next-generation sequencing of the Chrysanthemum nankingense (Asteraceae) transcriptome permits large-scale unigene assembly and SSR marker discovery. PLoS ONE 8:e62293. doi:10.1371/journal.pone.0062293
Information
  • Publisher :KOREAN SOCIETY FOR HORTICULTURAL SCIENCE
  • Publisher(Ko) :원예과학기술지
  • Journal Title :Horticultural Science and Technology
  • Journal Title(Ko) :원예과학기술지
  • Volume : 36
  • No :1
  • Pages :108-114
  • Received Date : 2017-08-25
  • Revised Date : 2017-10-02
  • Accepted Date : 2017-09-28
  • DOI :https://doi.org/10.12972/kjhst.20180012
Journal Informaiton Horticultural Science and Technology Horticultural Science and Technology
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