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2014 Vol.32, Issue 4 Preview Page
Single Nucleotide Polymorphism Marker Discovery from Transcriptome Sequencing for Marker-assisted Backcrossing in Capsicum
Jin-Ho Kang123
,
Hee-Bum Yang123
,
Hyeon-Seok Jeong123
,
Phillip Choe123
,
Jin-Kyung Kwon123
,
Byoung-Cheorl Kang123*
1Department of Plant Science, Seoul National University,
2Vegetable Breeding Research Center, Seoul National University
3Research Institute for Agriculture and Life Sciences, Seoul National University
*교신저자. *Corresponding Author. 
31 August 2014. pp. 535-543
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Abstract

Backcross breeding is the method most commonly used to introgress new traits into elite lines. Conventional backcross breeding requires at least 4-5 generations to recover the genomic background of the recurrent parent. Marker-assisted backcrossing (MABC) represents a new breeding approach that can substantially reduce breeding time and cost. For successful MABC, highly polymorphic markers with known positions in each chromosome are essential. Single nucleotide polymorphism (SNP) markers have many advantages over other marker systems for MABC due to their high abundance and amenability to genotyping automation. To facilitate MABC in hot pepper (Capsicum annuum), we utilized expressed sequence tags (ESTs) to develop SNP markers in this study. For SNP identification, we used Bukang F1-hybrid pepper ESTs to prepare a reference sequence through de novo assembly. We performed large-scale transcriptome sequencing of eight accessions using the Illumina Genome Analyzer (IGA) IIx platform by Solexa, which generated small sequence fragments of about 90-100 bp. By aligning each contig to the reference sequence, 58,151 SNPs were identified. After filtering for polymorphism, segregation ratio, and lack of proximity to other SNPS or exon/intron boundaries, a total of 1,910 putative SNPs were chosen and positioned to a pepper linkage map. We further selected 412 SNPs evenly distributed on each chromosome and primers were designed for high throughput SNP assays and tested using a genetic diversity panel of 27 Capsicum accessions. The SNP markers clearly distinguished each accession. These results suggest that the SNP marker set developed in this study will be valuable for MABC, genetic mapping, and comparative genome analysis.

Keywords
expressed sequence tag
linkage map
marker-assisted breeding

References
1
Anney, R.J., E. Kenny, C.T. O'Dushlaine, and J. Lasky-Su. 2008. Non-random error in genotype calling procedures: implications for family-based and case-control genome-wide association studies. Am. J. Med. Genet. B. 147B:1379-1386.
2
Ashrafi, H., T. Hill, K. Stoffel, A. Kozik, J. Yao, S.R. Chin-Wo, and A. Van Deynze. 2012. De novo assembly of the pepper transcriptome (Capsicum annuum): A benchmark for in silico discovery of SNPs, SSRs and candidate genes. BMC Genomics 13:571.
3
Blum, E., K. Liu, M. Mazourek, E.Y. Yoo, M. Jahn, and I. Paran. 2002. Molecular mapping of the C locus for presence of pungency in Capsicum. Genome 45:702-705.
4
Flicek, P. and E. Birney. 2009. Sense from sequence reads: Methods for alignment and assembly. Nat. Methods 6:S6-S12.
5
Goff, S.A., D. Ricke, T.H. Lan, G. Presting, R. Wang, M. Dunn, J. Glazebrook, A. Sessions, P. Oeller, H. Varma, D. Hadley, D. Hutchison, C. Martin, F. Katagiri, B.M. Lange, T. Moughamer, Y. Xia, P. Budworth, J. Zhong, T. Miguel, U. Paszkowski, S. Zhang, M. Colbert, W.L. Sun, L. Chen, B. Cooper, S. Park, T.C. Wood, L. Mao, P. Quail, R. Wing, R. Dean, Y. Yu, A. Zharkikh, R. Shen, S. Sahasrabudhe, A. Thomas, R. Cannings, A. Gutin, D. Pruss, J. Reid, S. Tavtigian, J. Mitchell, G. Eldredge, T. Scholl, R.M. Miller, S. Bhatnagar, N. Adey, T. Rubano, N. Tusneem, R. Robinson, J. Feldhaus, T. Macalma, A. Oliphant, and S. Briggs. 2002. A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296:92-100.
6
Herzog, E. and M. Frisch. 2013. Efficient marker-assisted backcross conversion of seed-parent lines to cytoplasmic male sterility. Plant Breed. 132:33-41.
7
Imelfort, M., C. Duran, J. Batley, and D. Edwards. 2009. Discovering genetic polymorphisms in next-generation sequencing data. Plant Biotechnol. J. 7:312-317.
8
Johnson, M., I. Zaretskaya, Y. Raytselis, Y. Merezhuk, S. McGinnis, and T.L. Madden. 2008. NCBIBLAST: A better web interface. Nucleic Acid Res. 36:W5-W9.
9
Jones, E., W.-C. Chu, M. Ayele, J. Ho, Ed Bruggeman, K. Yourstone, A. Rafalski, O.S. Smith, M.D. McMullen, C. Bezawada, J. Warren, J. Babayev, S. Basu, and S. Smith. 2009. Development of single nucleotide polymorphism (SNP) markers for use in commercial maize (Zea mays L.) germplasm. Mol. Breed. 24:165-176.
10
Jung, J.K., S.W. Park, W.Y. Liu, and B.C. Kang. 2010. Discovery of single nucleotide polymorphism in Capsicum and SNP markers for cultivar identification. Euphytica 175:91-107.
11
Kang, B.C., S.H. Nahm, J.H. Huh, H.S. Yoo, J.W. Yu, M.H. Lee, and B.D. Kim. 2001. An interspecific (Capsicum annuum x C. chinese) F2 linkage map in pepper using RFLP and AFLP markers. Theor. Appl. Genet. 102:531-539.
12
Kim, H.J., K.H. Baek, S.W. Lee, J. Kim, B.W. Lee, H.S. Cho, W.T. Kim, D. Choi, and C.G. Hur. 2008. Pepper EST database: comprehensive in silico tool for analyzing the chili pepper (Capsicum annuum) transcriptome. BMC Plant Biol. 8:101.
13
Kota, R., R.K. Varshney, T. Thiel, K.J. Dehmer, and A. Graner. 2001. Generation and comparison of EST-derived SSRs and SNPs in barley (Hordeurn vulgare L.). Hereditas 135:145-151.
14
Labate, J.A. and A.M. Baldo. 2005. Tomato SNP discovery by EST mining and resequencing. Mol. Breed. 16:343-349.
15
Lee, M.J., B.M. Popkin, and S. Kim. 2002. The unique aspects of the nutrition transition in South Korea: The retention of healthful elements in their traditional diet. Public Health Nutr. 5:197-203.
16
Li, H. and R. Durbin. 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754-1760.
17
Li, H., B. Handsaker, A. Wysoker, T. Fennell, J. Ruan, N. Homer, G. Marth, G. Abecasis, R. Durbin, and 1000 Genome Project Data Processing Subgroup. 2009. The sequence alignment/map format and SAMtools. Bioinformatics 25:2078-2079.
18
McPherson, J.D. 2009. Next-generation gap. Nat. Methods 6:S2-S5.
19
Metzker, M.L. 2005. Emerging technologies in DNA sequencing. Genome Res. 15:1767-1776.
20
Metzker, M.L. 2010. Sequencing technologies - The next generation. Genetics 11:31-46.
21
Nicolai, M., C. Pisani, J.P. Bouchet, M. Vuylsteke, and A. Palloix. 2012. Discovery of a large set of SNP and SSR genetic markers by high-throughput sequencing of pepper (Capsicum annuum). Genet. Mol. Res. 11:2295-2300.
22
Nielsen, R., J.S. Paul, A. Albrechtsen, and Y.S. Song. 2011. Genotype and SNP calling from next-generation sequencing data. Nat. Rev. Genet. 12:443-451.
23
Paran, I., J.R. van der Voort, V. Lefebvre, M. Jahn, L. Landry, M. van Schriek, B. Tanyolac, C. Caranta, A.B. Chaim, K. Livingstone, A. Palloix, and J. Peleman. 2004. An integrated genetic linkage map of pepper (Capsicum spp.). Mol. Breed. 13:251-261.
24
Perrier, X., A. Flori, and F. Bonnot. 2003. Data analysis methods, p. 43-46. In: P. Hamon, M. Seguin, X. Perrier, and J.C. Glaszmann. (eds.). Genetic diversity of cultivated tropical plants. Gifield Science Publishers, Montpellier.
25
Pettersson, F., A.P. Morris, M.R. Barnes, and L.R. Cardon. 2008. Goldsurfer2 (Gs2): A comprehensive tool for the analysis and visualization of genome wide association studies. BMC Bioinformatics 9:138.
26
Pompanon, F., A. Bonin, E. Bellemain, and P. Taberlet. 2005. Genotyping errors: Causes. Consequences and solutions. Nat. Rev. Genet. 6:847-859.
27
Rudd, S. 2003. Expressed sequence tags: alternative or complement to whole genome sequences? Trends Plant Sci. 8:321-329.
28
Shao, G.C., Z.Y. Zhang, N. Liu, S.E. Yu, and W.G. Xing. 2008. Comparative effects of deficit irrigation (DI) and partial rootzone drying (PRD) on soil water distribution, water use, growth and yield in greenhouse grown hot pepper. Sci. Hortic. 119:11-16.
29
Shendure, J. and H.L. Ji. 2008. Next-generation DNA sequencing. Nat. Biotechnol. 26:1135-1145.
30
Teo, Y.Y., A.E. Fry, T.G. Clark, E.S. Tai, and M. Seielstad. 2007. Data sheet: Sentrix HumanHap550 genotyping BeadChip. Ann. Hum. Genet. 71:701-703.
31
The Arabidopsis Genome Initiative. 2000. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796-815.
32
Varshney, R.K., S.N. Nayak, G.D. May, and S.A. Jackson. 2009. Next-generation sequencing technologies and their implications for crop genetics and breeding. Trends Biotechnol. 27:522-530.
33
Vignal, A., D. Milan, M. SanCristobal, and A. Eggen. 2002. A review on SNP and other types of molecular markers and their use in animal genetics. Genet. Sel. Evol. 34:275-305.
34
Wahyuni, Y., A.R. Ballester, E. Sudarmonowati, R.J. Bino, and A.G. Bovy. 2011. Metabolite biodiversity in pepper (Capsicum) fruits of thirty-two diverse cultivars: Variation in health-related compounds and implications for breeding. Phytochemistry 72: 1358-1370.
35
Wahyuni, Y., A.R. Ballester, Y. Tikunov, R.C.H. de Vos, K.T.B. Pelgrom, A. Maharijaya, E. Sudarmonowati, R.J. Bino, and A.G. Bovy. 2013. Metabolomics and molecular marker analysis to explore pepper (Capsicum sp.) biodiversity. Metabolomics 9:130-144.
36
Weiss, E.A. 2002. Spice crops. CABI Publishing International, Oxon, UK p. 7-22.
37
Wittenberger, T., H.C. Schaller, and S. Hellebrand. 2001. An expressed sequence tag (EST) data mining strategy succeeding in the discovery of new G-protein coupled receptors. J. Mol. Biol. 307:799-813.
38
Yang, H.B., W.Y. Liu, W.H. Kang, M. Jahn, and B.C. Kang. 2009. Development of SNP markers linked to the L locus in Capsicum spp. by a comparative genetic analysis. Mol. Breed. 24:433-446.
39
Yang, H.B., W.Y. Liu, W.H. Kang, J.H. Kim, H.J. Cho, J.H. Yoo, and B.C. Kang. 2012. Development and validation of L allele- specific markers in Capsicum. Mol. Breed.30:819-829.
40
Yi, G.B., J.M. Lee, S. Lee, D. Choi, and B.D. Kim. 2006. Exploitation of pepper EST-SSRs and an SSR-based linkage map. Theor. Appl. Genet. 114:113-130.
41
Yoo, E.Y., S. Kim, Y.H. Kim, C.J. Lee, and B.D. Kim. 2003. Construction of a deep coverage BAC library from Capsicum annuum, ‘CM334’. Theor. Appl. Genet. 107:540-543.
Information
  • Publisher :KOREAN SOCIETY FOR HORTICULTURAL SCIENCE
  • Publisher(Ko) :한국원예학회
  • Journal Title :Horticultural Science and Technology
  • Journal Title(Ko) :원예과학기술지
  • Volume : 32
  • No :4
  • Pages :535-543
  • Received Date : 2014-06-17
  • Revised Date : 2014-07-07
  • Accepted Date : 2014-07-08
  • DOI :https://doi.org/10.7235/hort.2014.14109
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