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Single Nucleotide Polymorphism Marker Discovery from Transcriptome Sequencing for Marker-assisted Backcrossing in Capsicum

  • 투고 : 2014.06.17
  • 심사 : 2014.07.08
  • 발행 : 2014.09.30

초록

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 $F_1$-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.

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참고문헌

  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. https://doi.org/10.1002/ajmg.b.30836
  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. https://doi.org/10.1186/1471-2164-13-571
  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. https://doi.org/10.1139/g02-031
  4. Flicek, P. and E. Birney. 2009. Sense from sequence reads: Methods for alignment and assembly. Nat. Methods 6:S6-S12. https://doi.org/10.1038/nmeth.1376
  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. https://doi.org/10.1126/science.1068275
  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. https://doi.org/10.1111/pbr.12021
  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. https://doi.org/10.1111/j.1467-7652.2009.00406.x
  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. https://doi.org/10.1093/nar/gkn201
  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. https://doi.org/10.1007/s11032-009-9281-z
  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. https://doi.org/10.1007/s10681-010-0191-2
  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) $F_2$ linkage map in pepper using RFLP and AFLP markers. Theor. Appl. Genet. 102:531-539. https://doi.org/10.1007/s001220051678
  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. https://doi.org/10.1186/1471-2229-8-101
  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. https://doi.org/10.1007/s11032-005-1911-5
  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. https://doi.org/10.1093/bioinformatics/btp324
  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. https://doi.org/10.1093/bioinformatics/btp352
  18. McPherson, J.D. 2009. Next-generation gap. Nat. Methods 6:S2-S5. https://doi.org/10.1038/nmeth.f.268
  19. Metzker, M.L. 2005. Emerging technologies in DNA sequencing. Genome Res. 15:1767-1776. https://doi.org/10.1101/gr.3770505
  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. https://doi.org/10.4238/2012.August.13.3
  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. https://doi.org/10.1038/nrg2986
  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. https://doi.org/10.1023/B:MOLB.0000022526.30914.31
  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. https://doi.org/10.1186/1471-2105-9-138
  26. Pompanon, F., A. Bonin, E. Bellemain, and P. Taberlet. 2005. Genotyping errors: Causes. Consequences and solutions. Nat. Rev. Genet. 6:847-859. https://doi.org/10.1038/nrg1707
  27. Rudd, S. 2003. Expressed sequence tags: alternative or complement to whole genome sequences? Trends Plant Sci. 8:321-329. https://doi.org/10.1016/S1360-1385(03)00131-6
  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. https://doi.org/10.1016/j.scienta.2008.07.001
  29. Shendure, J. and H.L. Ji. 2008. Next-generation DNA sequencing. Nat. Biotechnol. 26:1135-1145. https://doi.org/10.1038/nbt1486
  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. https://doi.org/10.1111/j.1469-1809.2007.00356.x
  31. The Arabidopsis Genome Initiative. 2000. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796-815. https://doi.org/10.1038/35048692
  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. https://doi.org/10.1016/j.tibtech.2009.05.006
  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. https://doi.org/10.1186/1297-9686-34-3-275
  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. https://doi.org/10.1016/j.phytochem.2011.03.016
  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. https://doi.org/10.1007/s11306-012-0432-6
  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. https://doi.org/10.1006/jmbi.2001.4520
  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. https://doi.org/10.1007/s11032-009-9304-9
  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 allelespecific markers in Capsicum. Mol. Breed.30:819-829. https://doi.org/10.1007/s11032-011-9666-7
  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. https://doi.org/10.1007/s00122-006-0415-y
  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. https://doi.org/10.1007/s00122-003-1279-z

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