Varietal identification of tea (Camellia sinensis) using nanofluidic array of single nucleotide polymorphism (SNP) markers

Horticulture Research

Volumn 1, Issue , 2014, Pages

  Fang, Wan Ping ^a,b   Meinhardt, Lyndel W ^b   Tan, Hua Wei ^a   Zhou, Lin ^a   Mischke, Sue ^b   Zhang, Dapeng ^b  

^a NANJING AGRICULTURAL UNIVERSITY   (China)

^b AGRICULTURAL RESEARCH SERVICE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 85009077852     PISSN: None     EISSN: 20527276     Source Type: Journal    
DOI: 10.1038/hortres.2014.35     Document Type: Article

References (50)

1. Macfarlane A, Macfarlane I. The Empire of Tea. New York: The Overlook Press, 2004; 32.
2. Barua PK. Classification of the tea plant. Two Bud 1963; 10: 3-11.
3. Ming TL, Bartholomew B. Theaceae. In: Wu ZY, Raven PH, Hong DY, (eds.) Flora of China. Beijing/St Louis, MO: Science Press & Missouri Botanical Garden Press, 2007: 367.
4. Kingdon-Ward F. Does wild tea exist? Nature 1950; 4191: 297-299.
5. Chang HT, Bartholomew B. Camellias. Portland, OR: Timber Press, 1984.
6. Kulasegaram S. Progress in tea breeding. Trop Agric Res Ser 1978; 11: 151-160.
7. Heiss ML, Heiss RJ. The Story of Tea: A Cultural History and a Drinking Guide. Berkley, CA: Ten Speed Press, 2007: 417.
8. Luypaert J, Zhang MH, Massart DL. Feasibility study for the use of near infrared spectroscopy in the qualitative and quantitative analysis of green tea, Camellia sinensis (L.). Anal Chim Acta 2003; 478: 303-312.
9. Zhang MH, Luypaert J, Fernández Pierna JA et al. Determinationoftotal antioxidant capacity in green tea by near-infrared spectroscopy and multivariate calibration. Talanta 2004; 62: 25-35.
10. Chen QS, Zhao JW, Liu MH et al. Determination of total polyphenols content in green tea using FT-NIR spectroscopy and different PLS algorithms. J Pharmaceut Biomed 2008; 46: 568-573.
11. He Y, Li XL, Deng XF. Discrimination of varieties of tea using near infrared spectroscopy by principal component analysis and BP model. J Food Eng 2007; 79: 1238-1242.
12. Tan SM, Luo RM, Zhou YP et al. Boosting partial least-squares discriminant analysis with application to near infrared spectroscopic tea variety discrimination. J Chemometr 2012; 26: 34-39.
13. Stoeckle MY, Gamble CC, Kirpekar R et al. Commercial teas highlight plant DNA barcode identification successes and obstacles. Sci Rep 2011; 1: 42.
14. Ujihara T, Ohta R, Hayashi N et al. Identification of Japanese and Chinese green tea cultivars by using simple sequence repeat markers to encourage proper labeling. Biosci Biotechnol Biochem 2009; 73: 15-20.
15. Ujihara T, Hayashi N, Tanaka J. Identification of material cultivar of green tea infusions by simple sequence repeat markers. Food Sci Technol Res 2012; 18: 209-217.
16. Kaundun SS, Matsumoto S. PCR-based amplicon length polymorphisms (ALPs) at microsatellite loci and indels from non-coding DNA regions of cloned genes as a means of authenticating commercial Japanese green teas. JSci Food Agric 2004; 84: 895-902.
17. Chen L, Zhou ZX, Yang YJ. Genetic improvement and breeding of tea plant (Camellia sinensis) in China: from individual selection to hybridization and molecular breeding. Euphytica 2007; 154: 239-248.
18. Ma JQ, Zhou YH, Ma CL et al. Identification and characterization of 74 novel polymorphic EST-SSR markers in the tea plant, Camellia sinensis (Theaceae). Am J Bot 2010; 97: 153-156.
19. Sharma P, Kumar S. Differential display-mediated identification of three drought-responsive expressed sequence tags in tea [Camellia sinensis (L.) O. Kuntze]. J Bioscience 2005; 30: 231-235.
20. Taniguchi F, Fukuoka H, Tanaka J. Expressed sequence tags from organ-specific cDNA libraries of tea (Camellia sinensis) and polymorphisms and transferability of EST-SSRs across Camellia species. Breed Sci 2012; 62: 186-195.
21. Yang JB, Yang J, Li HT et al. Isolation and characterization of 15 microsatellite markers from wild tea plant (Camellia taliensis) using FIASCO method. Conserv Genet 2009; 10: 1621-1623.
22. Zhao LP, Liu Z, Chen L et al. Generation and characterization of 24 novel EST derived microsatellites from tea plant (Camellia sinensis) and cross-species amplification in its closely related species and varieties. Conserv Genet 2008; 9: 1327-1331.
23. Ujihara T, Taniguchi F, Tanaka J et al. Development of expressed sequence tag (EST)-based cleaved amplified polymorphic sequence (CAPS) markers of tea plant and their application to cultivar identification. J Agric Food Chem 2011; 59: 1557-1564.
24. Hu CY, Tsai YZ, Lin SF. Development of STS and CAPS markers for variety identification and genetic diversity analysis of tea germplasm in Taiwan. Bot Stud 2014; 55: 12.
25. Weising K, Nybom H, Pfenninger M et al. DNA Fingerprinting in Plants: Principles, Methods, and Applications. 2nd ed. Boca Raton, FL: CRC Press, 2005.
26. Buckler ES, Thornsberry J. Plant molecular diversity and applications to genomics. Curr Opin Plant Biol 2002; 5: 107-111.
27. Zhang DX, Hewitt GM. Nuclear DNA analyses in genetic studies of populations: practice, problems and prospects. Mol Ecol 2003; 12: 563-584.
28. Fang WP, Meinhardt LW, Mischke S et al. Accurate determination of genetic identity for a single cacao bean, using molecular markers with a nanofluidic system, ensures cocoa authentication. J Agric Food Chem 2014; 62: 481-487.
29. Tanaka J, Taniguchi F, Hirai N et al. Estimation of the genome size of tea (Camellia sinensis), camellia (C. japonica), and their interspecific hybrids by flow cytometry. Tea Res J 2006; 101: 1-7.
30. Chen J, Wang PS, Xia YM et al. Genetic diversity and differentiation of Camellia sinensis L. (cultivated tea) and its wild relatives in Yunnan province of China, revealed by morphology, biochemistry and allozyme studies. Genet Resources Crop Evol 2005; 52: 41-52.
31. Park JS, Kim JB, Hahn BS et al. EST analysis of genes involved in secondary metabolism inCamellia sinensis (tea), using suppression subtractive hybridization. Plant Sci 2004; 166: 953-961.
32. Shi CY, Yang H, Wei CL et al. Deep sequencing of the Camellia sinensis transcriptome revealed candidate genes for major metabolic pathways of tea-specific compounds. BMC Genomics 2011; 12: 131.
33. Li WZ, Godzik A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 2006; 22: 1658-1659.
34. Tang JF, Vosman B, Voorrips RE et al. QualitySNP: a pipeline for detecting single nucleotide polymorphisms and insertions/deletions in EST data from diploid and polyploid species. BMC Bioinformatics 2006; 7: 438.
35. McCouch SR, Zhao KY, Wright M et al. Development of genome-wide SNP assays for rice. Breeding Sci 2010; 60: 524-535.
36. Wang J, Lin M, Crenshaw A et al. High-throughput single nucleotide polymorphism genotyping using nanofluidic Dynamic Arrays. BMC Genomics 2009; 10: 561.
37. Fluidigm. Fluidigm SNP Genotyping User Guide Rev H1, PN 68000098. South San Francisco, CA: Fluidigm Corporation, 2011.
38. Evett IW, Weir BS. Interpreting DNA Evidence: Statistical Genetics for Forensic Scientists. Sunderland, MA: Sinauer, 1998.
39. Peakall R, Smouse PE. Genalex 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol Ecol Notes 2006; 6: 288-295.
40. Peakall R. Smouse PE. GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research-an update. Bioinformatics 2012; 28: 2537-2539.
41. Waits LP, Luikart G, Taberlet P. Estimating the probability of identity among genotypes in natural populations: cautions and guidelines. Mol Ecol 2001; 10: 249-256.
42. Peakall R, Smouse PE, Huff DR. Evolutionary implications of allozyme and RAPD variation in diploid populations of dioecious buffalograss Buchloe dactyloides. Mol Ecol 1995; 4: 135-147.
43. Pritchard JK, Stephens M, Donnelly P. Inference of population structure using multilocus genotype data. Genetics 2000; 155: 945-959.
44. Evanno G, Regnaut S, Goudet J et al. Detecting the number of clusters ofindividuals using the software STRUCTURE: a simulation study. Mol Ecol 2005; 14: 2611-2620.
45. Earl DA, vonHoldt BM. STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv Genet Resources 2012; 4: 359-361.
46. Yao MZ, Ma CL, Qiao TT et al. Diversity distribution and population structure of tea germplasms in China revealed by EST-SSR markers. Tree Genet Genomes 2012; 8: 205-220.
47. Maughan PJ, Smith SM, Rojas-Beltran JA et al. Single nucleotide polymorphism identification, characterization, and linkage mapping in quinoa. Plant Genome 2012; 5: 114-125.
48. Maughan PJ, Smith SM, Fairbanks DJ et al. Development, characterization, and linkage mapping of single nucleotide polymorphisms in the Grain Amaranths (Amaranthus sp.). Plant Genome 2011; 4: 92-101.
49. Longhi S, Giongo L, Buti M et al. Molecular genetics and genomics of the Rosoideae: state of the art and future perspectives. Hort Res 2014; 1: 1.
50. Zhao DW, Yang JB, Yang SX et al. Genetic diversity and domestication origin of tea plantCamellia taliensis (Theaceae) as revealed by microsatellite markers. BMC Plant Biol 2014; 14: 14.