Discovery of single nucleotide polymorphism in Capsicum and SNP markers for cultivar identification

Euphytica

Volumn 175, Issue 1, 2010, Pages 91-107

  Jung, Jin kee ^a,b   Park, Soung Woo ^a   Liu, Wing Yee ^a   Kang, Byoung Cheorl ^a  

^a Seoul National University   (South Korea)

^b Ministry of Agriculture and Forestry Korea   (South Korea)

Author keywords

Allele specific PCR; Capsicum; Conserved ortholog set; Cultivar identification; Single nucleotide polymorphism

Indexed keywords

ARABIDOPSIS; CAPSICUM; CAPSICUM ANNUUM; CAPSICUM ANNUUM VAR. ANNUUM; CAPSICUM CHINENSE; LYCOPERSICON ESCULENTUM;

EID: 77955174748     PISSN: 00142336     EISSN: 15735060     Source Type: Journal    
DOI: 10.1007/s10681-010-0191-2     Document Type: Article

References (72)

1. Arabidopsis_Genome_Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408: 796-815.
2. Ben Chaim A, Paran I, Grube R, Jahn M, van Wijk R, Peleman J (2001) QTL mapping of fruit related traits in pepper (Capsicum annuum). Theor Appl Genet 102: 1016-1028.
3. Benor S, Zhang M, Wang Z, Zhang H (2008) Assessment of genetic variation in tomato (Solanum lycopersicum L.) inbred lines using SSR molecular markers. J Genet Genomics 35: 373-379.
4. Bertin I, Zhu JH, Gale MD (2005) SSCP-SNP in pearl millet-a new marker system for comparative genetics. Theor Appl Genet 110: 1467-1472.
5. Caranta C, Pflieger S, Lefebvre V, Daubè ze AM, Thabuis A, Palloix A (2002) QTLs involved in the restriction of cucumber mosaic virus (CMV) long-distance movement in pepper. Theor Appl Genet 104: 586-591.
6. Ching A, Caldwell KS, Jung M, Dolan M, Smith OS, Tingey S, Morgante M, Rafalski AJ (2002) SNP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines. BMC Genet 3: 1-14.
7. Denyze AV, Stoffel K, Buell CR, Kozik A, Liu J, van der Knaap E, Francis D (2007) Diversity in conserved genes in tomato. BMC Genomics 8: 465-473.
8. Desai UJ, Pfaffle PK (1995) Single-step purification of a thermostable DNA polymerase expressed in Escherichia coli. Biotechniques 19: 780-782, 784.
9. Drenkard E, Richter BG, Rozen S, Stutius LM, Angell NA, Mindrinos M, Cho RJ, Oefner PJ, Davis RW, Ausubel FM (2000) A simple procedure for the analysis of single nucleotide polymorphisms facilitates map-based cloning in Arabidopsis. Plant Physiol 124: 1483-1492.
10. Dyer GA, Taylor JE (2008) A crop population perspective on maize seed systems in Mexico. PNAS 105: 470-475.
11. Feltus FA, Wan J, Schulze SR, Estill JC, Jiang N, Paterson AH (2004) An SNP resource for rice genetics and breeding based on subspecies indica and japonica genome alignments. Genome Res 14: 1812-1819.
12. Feltus FA, Singh HP, Lohithaswa HC, Schulze SR, Silva TD, Paterson AH (2006) A comparative genomics strategy for targeted discovery of single-nucleotide polymorphisms and conserved-noncoding sequences in orphan crops. Plant Physiol 140: 1183-1191.
13. Fulton TM, van der Hoeven R, Eannetta NT, Tanksley SD (2002) Identification, analysis, and utilization of conserved ortholog set markers for comparative genomics in higher plants. Plant Cell 14: 1457-1467.
14. Garces-Claver A, Fellman SM, Gil-Ortega R, Jahn M, Arnedo-Andres MS (2007) Identification, validation and survey of a single nucleotide polymorphism (SNP) associated with pungency in Capsicum spp. Theor Appl Genet 115: 907-916.
15. Gilchrist EJ, Haughn GW, Ying CC, Otto SP, Zhuang J, Cheung D, Hamberger B, Aboutorabi F, Kalynyak T, Johnson L, Bohlmann J, Ellis BE, Douglas CJ, Cronk QCB (2006) Use of Ecotilling as an efficient SNP discovery tool to survey genetic variation in wild populations of Populus trichocarpa. Mol Ecol 15: 1367-1378.
16. TA GENE: multipopulation integrated genetic and radiation hybrid mapping. Bioinformatics 21(8): 1703-1704.
17. Goff SA, Ricke D, Lan TH, Presting G, Wang R, Dunn M, Glazebrook J, Sessions A, Oeller P, Varma H, Hadley D, Hutchison D, Martin C, Katagiri F, Lange BM, Moughamer T, Xia Y, Budworth P, Zhong J, Miguel T, Paszkowski U, Zhang S, Colbert M, Sun WL, Chen L, Cooper B, Park S, Wood TC, Mao L, Quail P, Wing R, Dean R, Yu Y, Zharkikh A, Shen R, Sahasrabudhe S, Thomas A, Cannings R, Gutin A, Pruss D, Reid J, Tavtigian S, Mitchell J, Eldredge G, Scholl T, Miller RM, Bhatnagar S, Adey N, Rubano T, Tusneem N, Robinson R, Feldhaus J, Macalma T, Oliphant A, Briggs S (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296: 92-100.
18. Hayashi K, Hashimoto N, Daigen M, Ashikawa I (2004) Development of PCR-based SNP markers for rice blast resistance genes at the Piz locus. Theor Appl Genet 108(7): 1212-1220.
19. Hwang J, Li J, Liu W, An SJ, Cho H, Her NH, Yeam I, Kim D, Kang BC (2009) Double mutation in eIF4E and eIFiso4E confer recessive resistance to Chilli Veinal Mottle Virus in pepper. Mol Cells 27: 329-336.
20. Jackson DA, Somers KM, Harvey HH (1989) Similarity coefficients: measures of co-occurrence and association or simply measure of occurrence? Am Nat 133: 436.
21. 2 linkage map in pepper using RFLP and AFLP markers. Theor Appl Genet 102(4): 531-539.
22. Kim S, Misra A (2007) SNP genotyping: technologies and biomedical applications. Annu Rev Biomed Eng 9: 289-320.
23. Kwok PY (2001) Methods for genotyping single nucleotide polymorphism. Annu Rev Genomics Hum Genet 2: 235-258.
24. Kwon YS, Lee JM, Yi GB, Yi SI, Kim KM, Soh EH, Bae KM, Park EK, Song IH, Kim BD (2005) Use of SSR markers to complement tests of distinctiveness, uniformity, and stability (DUS) of pepper (Capsicum annuum L.) varieties. Mol Cells 30: 428-435.
25. Labate JA, Baldo AM (2005) Tomato SNP discovery by EST mining and resequencing. Mol Breeding 16: 343-349.
26. Lai E, Bowman C, Bansal A, Hughes A, Mosteller M, Roses AD (2002) Medical applications of haplotype-based SNP maps: learning to walk before we run. Nat Genet 32: 353.
27. Landegren U, Kaiser R, Caskey CT (1988) DNA diagnostics-molecular techniques and automation. Science 242: 229-237.
28. Le Hellard S, Ballereau SJ, Visscher PM, Torrance HS, Pinson J (2002) SNP genotyping on pooled DNAs: comparison of genotyping technologies and a semi automated method for data storage and analysis. Nucleic Acids Res 30: e74.
29. Lee JM, Nahm SH, Kim YM, Kim BD (2004) Characterization and molecular genetic mapping of microsatellite loci in pepper. Theor Appl Genet 108: 619-627.
30. Lefebvre V, Palloix A, Rives M (1993) Nuclear RFLP between pepper cultivars (Capsicum annuum L.). Euphytica 71(3): 189.
31. Lefebvre V, Palloix A, Caranta C, Pochard E (1995) Construction of an intraspecific integrated linkage map of pepper using molecular markers and doubled-haploid progenies. Genome 38: 112.
32. Lefebvre V, Goffinet B, Chauvet JC (2001) Evaluation of genetic distances between pepper inbred lines for cultivar protection purposes: comparison of AFLP, RAPD and phenotypic data. Theor Appl Genet 102(5): 741-750.
33. Lefebvre V, Pflieger S, Tabuis A, Caranta C, Blattes C, Chauvet JC, Caubeze AM, Palloix A (2002) Towards the saturation of the pepper linkage map by alignment of three intraspecific maps including known-function genes. Genome 45: 839-854.
34. Lijavetzky D, Cabezas JA, Ibanez A, Rodriguez V, Martinez-Zapater JM (2007) High throughput SNP discovery and genotyping in grapevine (Vitis vinifera L.) by combining a re-sequencing approach and SNPlex technology. BMC Genomics 8: 424.
35. Livak KJ, Flood SJ, Marmaro J (1995) Oligonucleotides with fluorescent dyes at opposite ends provide a quenched probe system useful for detecting PCR product and nucleic acid hybridization. PCR methods and applications 4(6): 357-362.
36. Livingstone KD, Lackney VK, Blauth JR, van Wijk R, Jahn MK (1999) Genome mapping in Capsicum and the evolution of genome structure in the Solanaceae. Genetics 152: 1183-1202.
37. Lorenzo B, Bonnet J, Boudet C, Signoret P, Nagy I, Lanteri S, Palloix A, Lefebvre V (2007) A high-resolution intraspecific linkage map of pepper (Capsicum annuum L.) and selection of reduced RIL subsets for fast mapping. Genome 50: 51-60.
38. Martins-Lopes P, Zhang H, Koebner R (2001) Detection of single nucleotide mutations in wheat using single strand conformation polymorphism gels. Plant Molecular Biology Reporter 19: 159-162.
39. Minamiyama Y, Tsuro M, Hirai M (2006) An SSR-based linkage map of Capsicum annuum. Mol Breeding 18: 157-169.
40. Morales M, Roig E, Monforte AJ, Arus P, Garcia-Mas J (2004) Single-nucleotide polymorphisms detected in expressed sequence tags of melon (Cucumis melo L.). Genome 47: 352-360.
41. Moury B, Pflieger S, Blattes A, Lefebvre V, Palloix A (2000) A CAPS marker to assist selection of tomato spotted wilt virus (TSWV) resistance in pepper. Genome 43: 137-142.
42. Paran I, Aftergoot E, Shifriss C (1998) Variation in Capsicum annuum revealed by RAPD and AFLP markers. Euphytica 99: 167-173.
43. Park SW, An SJ, Yang HB, Kwon JK, Kang BC (2009) Optimization of high resolution melting analysis and discovery of single nucleotide polymorphism in Capsicum. Hort Environ Biotechnol 50: 31-39.
44. Peakall R, Smouse PE (2006) GENALEX 6. 1: genetic analysis in excel. Population genetic software for teaching and research. Mol Ecol Notes 6: 288-295. http://www. blackwell-synergy. com/doi/abs/10. 1111/j. 1471-8286. 2005. 01155. x. Accessed 23 Oct 2008.
45. Portis E, Nagy I, Sasvári Z, Stágel A, Barchi L, Lanteri S (2007) The design of Capsicum spp. SSR assays via analysis of in silico DNA sequence, and their potential utility for genetic mapping. Plant Sci 172: 640-648.
46. Prince JP, Lackney VK, Angeles C (1995) A survey of DNA polymorphism within the genus Capsicum and the fingerprinting of pepper cultivars. Genome 38(2): 224.
47. Rafalski A (2002) Applications of single nucleotide polymorphisms in crop genetics. Curr Opin Plant Biol 5: 94-100.
48. Rahman M, McVetty PB, Li G (2007) Development of SRAP, SNP and multiplexed SCAR molecular markers for the major seed coat color gene in Brassica rapa L. Theor Appl Genet 115: 1101-1107.
49. Ramirez M, Graham MA, Blanco-Lopez L, Silvente S, Medrano-Soto A, Blair MW, Hernandez G, Vance CP, Lara M (2005) Sequencing and analysis of common bean ESTs. Building a foundation for functional genomics. Plant Physiol 137: 1211-1227.
50. Reale S, Doveri S, Diaz A, Angiolillo A, Lucentini L, Pilla F, Martin A, Donini P, Lee D (2006) SNP-based markers for discriminating olive (Olea europaea L.) cultivars. Genome 49: 1193-1205.
51. Rickert AM, Kim JH, Meyer S, Nagel A, Ballvora A, Oefner PJ, Gebhardt C (2003) First-generation SNP/InDel markers tagging loci for pathogen resistance in the potato genome. Plant Biotechnol J 1: 339-410.
52. Rostoks N, Mudie S, Cardle L, Russell J, Ramsay L, Booth A, Svensson JT, Wanamaker SI, Walia H, Rodriguez EM, Hedley PE, Liu H, Morris J, Close TJ, Marshall DF, Waugh R (2005) Genome-wide SNP discovery and linkage analysis in barley based on genes responsive to abiotic stress. Mol Genet Genomics 274: 515-527.
53. Sarri V, Baldoni L, Porceddu A, Cultrera NGM, Contento A, Frediani M, Belaj A, Trujillo I, Cionini PG (2008) Microsatellite markers are powerful tools for discriminating among olive cultivars and assigning them to geographically defined populations. Genome 49: 1606-1615.
54. Shirasawa K, Shiokai S, Yamaguchi M, Kishitani S, Nishio T (2006) Dot-blot-SNP analysis for practical plant breeding and cultivar identification in rice. Theor Appl Genet 113: 147-155.
55. Smýkal P, Horáèek J, Dostálová R, Hýbl M (2008) Variety discrimination in pea (Pisum sativum L.) by molecular, biochemical and morphological markers. J Appl Genet 49: 155-166.
56. Sneath PHA, Sokal RR (1973) Numerical taxonomy-the principles and practice of numerical classification. WH Freeman and Company, San Francisco, pp 230-234.
57. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22(22): 4673-4680.
58. Tondelli A, Francia E, Barabaschi D, Aprile A, Skinner JS, Stockinger EJ, Stanca AM, Pecchioni N (2006) Mapping regulatory genes as candidates for cold and drought stress tolerance in barley. Theor Appl Genet 112: 445-454.
59. Tu M, Lu BR, Zhu Y, Wang Y (2007) Abundant within-varietal genetic diversity in rice germplasm from Yunnan province of china revealed by SSR fingerprints. Biochem Genet 45: 789-801.
60. UPOV (2002) http://www. upov. int/index_en. html.
61. Vignal A, Milan D, SanCristobal M, Eggen A (2002) A review on SNP and other types of molecular markers and their use in animal genetics. Genet Sel Evol 34: 275-305.
62. Werner FA, Durstewitz G, Habermann FA (2004) Detection and characterization of SNPs useful for identity control and parentage testing in major European dairy breeds. Anim Genet 35(1): 44-49.
63. Wu F, Mueller LA, Crouzillat D, Petiard V, Tanksley SD (2006) Combining bioinformatics and phylogenetics to identify large sets of single-copy orthologous genes (COSII) for comparative, evolutionary and systematic studies: a test case in the euasterid plant clade. Genetics 174: 1407-1420.
64. Wu F, Eannetta NT, Xu Y, Durrett R, Mazourek M, Jahn MM, Tanksley SD (2009) A COSII genetic map of the pepper genome provides a detailed picture of synteny with tomato and new insights into recent chromosome evolution in the genus Capsicum. Theor Appl Genet 118: 1279-1293.
65. Yamamoto N, Tsugane T, Watanabe M, Yano K, Maeda F, Kuwata C, Torki M, Ban Y, Nishimura S, Shibata D (2005) Expressed sequence tags from the laboratory-grown miniature tomato (Lycopersicon esculentum) cultivar Micro-Tom and mining for single nucleotide polymorphisms and insertions/deletions in tomato cultivars. Gene 356: 127-134.
66. Yang W, Bai X, Kabelka E, Eaton C, Kamoun S, van der Kannp E, Francis D (2004) Discovery of single nucleotide polymorphisms in Lycopersicon esculentum by computer aided analysis of expressed sequence tags. Mol Breeding 14: 21-34.
67. Yi G, Lee JM, Lee S, Choi D, Kim BD (2006) Exploitation of pepper EST-SSRs and an SSR-based linkage map. Theor Appl Genet 114: 113-130.
68. Yoon JB, Do JW, Yang DC, Park HG (2004) Interspecific cross compatibility among five domesticated species of Capsicum genus. J Kor Soc Hort Sci 45: 324-329.
69. Yoon MS, Song QJ, Choi IY, Specht JE, Hyten DL, Cregan PB (2007) BARCSoySNP23: a panel of 23 selected SNPs for soybean cultivar identification. Theor Appl Genet 114: 885-899.
70. Yu J, Hu S, Wang J, Wong GK, Li S, Liu B, Deng Y, Dai L, Zhou Y, Zhang X, Cao M, Liu J, Sun J, Tang J, Chen Y, Huang X, Lin W, Ye C, Tong W, Cong L, Geng J, Han Y, Li L, Li W, Hu G, Huang X, Li W, Li J, Liu Z, Li L, Liu J, Qi Q, Liu J, Li L, Li T, Wang X, Lu H, Wu T, Zhu M, Ni P, Han H, Dong W, Ren X, Feng X, Cui P, Li X, Wang H, Xu X, Zhai W, Xu Z, Zhang J, He S, Zhang J, Xu J, Zhang K, Zheng X, Dong J, Zeng W, Tao L, Ye J, Tan J, Ren X, Chen X, He J, Liu D, Tian W, Tian C, Xia H, Bao Q, Li G, Gao H, Cao T, Wang J, Zhao W, Li P, Chen W, Wang X, Zhang Y, Hu J, Wang J, Liu S, Yang J, Zhang G, Xiong Y, Li Z, Mao L, Zhou C, Zhu Z, Chen R, Hao B, Zheng W, Chen S, Guo W, Li G, Liu S, Tao M, Wang J, Zhu L, Yuan L, Yang H (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296: 79-92.
71. Zhu T, Salmeron J (2007) High-definition genome profiling for genetic marker discovery. Trends Plant Sci 12: 196-202.
72. Zhu YL, Song QJ, Hyten DL, van Tassell CP, Matukumalli LK, Grimm DR, Hyatt SM, Fickus EW, Young ND, Cregan PB (2003) Single-nucleotide polymorphisms in soybean. Genetics 163: 1123-1134.