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Genetic diversity of oolong tea (Camellia sinensis) germplasms based on the nanofluidic array of single-nucleotide polymorphism (SNP) markers

Abstract

As one of the most popular Chinese tea products, oolong tea involves the most complicated manufacturing process and the most abundant tea germplasm resources. However, the unclear genetic backgrounds of oolong tea germplasms have been biological limitations for tea breeding and quality control. In this study, high-throughput SNP technology was used to analyze the genetic diversity of 100 oolong tea landraces and cultivars. Ninety-six pairs of primers were selected and validated from the expressed sequence tag (EST) database of Camellia sinensis. The results verified 75 SNP loci that are able to accurately and efficiently determine the genetic relationships among Chinese oolong tea germplasms. The DNA fingerprints of 4 main oolong tea-producing areas were constructed by tracing the information of each site of the SNP. The Guangdong oolong tea germplasms were a relatively distinct group, while the genotypes of Taiwan oolong tea were similar to those of populations in Fujian. The tea germplasms in Southern and Northern Fujian had the largest intersections, and they also showed their own characteristics. Our results provide guidance for the identification, integration, and selection of parents for tea plant germplasms. Moreover, our study provides an effective tool to protect the diversity of tea germplasms and to assist in future breeding work.

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References

  1. Aremu B, Babalola O (2015) Construction of specific primers for rapid detection of, South African exportable vegetable Macergens. Int J Environ Res Public Health 12(10):12356–12370. https://doi.org/10.3390/ijerph121012356

  2. Buckler ES, Thornsberry JM (2002) Plant molecular diversity and applications to genomics. Curr Opin Plant Biol 5:107–111. https://doi.org/10.1016/S1369-5266(02)00238-8

  3. Chen C (1970) The general history of tea plant. China Agriculture Press, Beijing

  4. Chen L, Gao QK, Chen DM, Xu CJ (2005) The use of RAPD markers for detecting genetic diversity, relationship and molecular identification of Chinese elite tea genetic resources [Camellia sinensis (L.) O. Kuntze] preserved in a tea germplasm repository. Biodivers Conserv 14(6):1433–1444. https://doi.org/10.1007/s10531-004-9787-y

  5. Chen L, Yamaguchi S (2010) RAPD markers for discriminating tea germplasms at the inter-specific level in China. Plant Breed 124(4):404–409. https://doi.org/10.1111/j.1439-0523.2005.0100.x

  6. Chen L, Yao MZ, Zhao LP, Wang XC (2006) Recent research progresses on molecular biology of tea plant (Camellia sinensis). Floriculture, ornamental and plant biotechnology: advances and topical issues. Lond Glob Sci Books 4:425–436

  7. Chen L, Zhou ZX, Yang YJ (2007) Genetic improvement and breeding of tea plant (Camellia sinensis) in China: from individual selection to hybridization and molecular breeding. Euphytica 154(1–2):239–248. https://doi.org/10.1007/s10681-006-9292-3

  8. Chen Q, Zhao J, Liu M, Cai J, Liu J (2008) Determination of total polyphenols content in green tea using FT-NIR spectroscopy and different PLS algorithms. J Pharm Biomed Anal 46(3):568–573. https://doi.org/10.1007/s10531-004-9787-y

  9. Chen S, Li M, Zheng G, Wang T, Jun L, Shanshan W et al (2018) Metabolite profiling of 14 Wuyi rock tea cultivars using UPLC-QTOF MS and UPLC-QqQ MS combined with chemometrics. Molecules 23:104–110. https://doi.org/10.3390/molecules23020104

  10. Das SC, Das S, Hazarika M (2012) Breeding of the tea plant (Camellia sinensis) in India. In: Chen L, Apostolides Z, Chen ZM (eds) Global tea breeding. Springer-Verlag, Berlin, pp 69–124

  11. Duan YS, Cheng H, Jiang YH, Wang LY, Zeng JM, Li XH (2010) Analysis of genetic diversity and relationship of oolong tea varieties and strains using SSR markers. J Tea Sci 30(2):141–148. https://doi.org/10.3724/SP.J.1238.2010.00512

  12. Earl DA, Vonholdt BM (2012) STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv Genet Resour 4(2):359–361. https://doi.org/10.1007/s12686-011-9548-7

  13. Evanno G, Regnaut S, Goudet J (2010) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14(8):2611–2620. https://doi.org/10.1111/j.1356-294x.2005.02553.x

  14. Fang W, Cheng H, Jiang X, Li X (2012) Genetic diversity and relationship of clonal tea (Camellia sinensis) cultivars in China as revealed by SSR markers. Plant Syst Evol 298(2):469–483. https://doi.org/10.1007/s00606-011-0559-3

  15. Fang WP, Meinhardt LW, Tan H, Zhou L, Mischke S, Wang X (2016) Identification of the varietal origin of processed loose-leaf tea based on analysis of a single leaf by SNP nanofluidic array. Crop J 4(4):304–312. https://doi.org/10.1016/j.cj.2016.02.001

  16. Fang WP, Meinhardt LW, Tan HW, Zhou L, Mischke S, Zhang D (2014) Varietal identification of tea (Camellia sinensis) using nanofluidic array of single nucleotide polymorphism (SNP) markers. Hortic Res 1:14035. https://doi.org/10.1038/hortres.2014.35

  17. Fu X, Chen Y, Mei X, Katsuno T, Kobayashi E, Dong F, Watanabe N, Yang Z (2015) Regulation of formation of volatile compounds of tea (Camellia sinensis) leaves by single light wavelength. Sci Rep 5:16858. https://doi.org/10.1038/srep16858

  18. Ganal MW, Altmann T, Roder MS (2009) SNP identification in crop plants. Curr Opin Plant Biol 12(2):211–217. https://doi.org/10.1016/j.pbi.2008.12.009

  19. Garrido-Cardenas JA, Mesa-Valle C, Manzano-Agugliaro F (2018) Trends in plant research using molecular markers. Planta 247(3):543–557. https://doi.org/10.1007/s00425-017-2829-y

  20. Gui J, Fu X, Zhou Y, Tsuyoshi K, Xin M, Rufang D et al (2015) Does enzymatic hydrolysis of glycosidically bound volatile compounds really contribute to the formation of volatile compounds during the oolong tea manufacturing process? J Agric Food Chem 63(31):6905–6914. https://doi.org/10.1021/acs.jafc.5b02741

  21. Han LK, Takaku T, Li J, Kimura Y, Okuda H (1999) Anti-obesity action of oolong tea. Int J Obes Relat Metab Disord 23(1):98–105. https://doi.org/10.1038/sj.ijo.0800766

  22. Hayat K, Iqbal H, Malik U, Bilal U, Mushtaq S (2015) Tea and its consumption: benefits and risks. Crit Rev Food Sci Nutr 55(7):939–954. https://doi.org/10.1080/10408398.2012.678949

  23. He Y, Li X, Deng X (2007) Discrimination of varieties of tea using near infrared spectroscopy by principal component analysis and BP model. J Food Eng 79(4):1238–1242. https://doi.org/10.1016/j.jfoodeng.2006.04.042

  24. Hu CY, Tsai YZ, Lin SF (2014) Development of STS and CAPS markers for variety identification and genetic diversity analysis of tea germplasm in Taiwan. Bot Stud 55:1999–3110 Artn 1210.1186/1999-3110-55-12

  25. Kim H, Yoon JB, Lee J (2017) Development of fluidigm SNPtype genotyping assays for marker-assisted breeding of chili pepper(Capsicum annuum L.). Korean J Horticult Sci 35:465–479. https://doi.org/10.12972/kjhst.20170050

  26. Konstantinidis KT, Stackebrandt E (2013) Defining taxonomic ranks. In: Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson FL (eds) The prokaryotes (4th edition): prokaryotic biology and symbiotic associations. Springer, Heidelberg, p 229

  27. Liu BY, Youyong LI, Tang YC, Wang LY, Cheng H, Wang PS (2010) Assessment of genetic diversity and relationship of tea germplasm in Yunnan as revealed by ISSR markers. Acta Agron Sin 36(3):391–400. https://doi.org/10.1016/S1875-2780(09)60037-7

  28. Liu Z, Chen Z, Guo H, He D, Zhao H, Wang Z et al (2016) The modulatory effect of infusions of green tea, oolong tea, and black tea on gut microbiota in high-fat-induced obese mice. Food Funct 7(12):4869–4879. https://doi.org/10.1039/c6fo01439a

  29. Ma JQ, Huang L, Ma CL, Jin JQ, Li CF, Wang RK, Zheng HK, Yao MZ, Chen L (2015) Large-scale SNP discovery and genotyping for constructing a high-density genetic map of tea plant using specific-locus amplified fragment sequencing (SLAF-seq). PLoS One 10(6):e0128798. https://doi.org/10.1371/journal.pone.0128798

  30. Meegahakumbura MK, Wambulwa MC, Thapa KK, Li MM, Möller M, Xu JC et al (2016) Indications for three independent domestication events for the tea plant (Camellia sinensis (L.) O. Kuntze) and new insights into the origin of tea germplasm in China and India revealed by nuclear microsatellites. PLoS One 11:e0155369. https://doi.org/10.1371/journal.pone.0155369

  31. Ministry of Agriculture and Rural Affairs of the People’s Republic of China (2019) Statistics on tea production and tea garden area in various regions of 2016. http://www.moa.gov.cn/. Accessed 1 June 2019

  32. Mondal TK, Bhattacharya A, Laxmikumaran M, Ahuja PS (2004) Recent advances of tea (Camellia Sinensis) biotechnology. Plant Cell Tissue Organ Cult 76(3):195–254. https://doi.org/10.1023/b:ticu.0000009254.87882.71

  33. Ng KW, Cao ZJ, Chen HB, Zhao ZZ, Zhu L, Yi T (2018) Oolong tea: a critical review of processing methods, chemical composition, health effects, and risk. Crit Rev Food Sci Nutr 58(17):2957–2980. https://doi.org/10.1080/10408398.2017.1347556

  34. Ohmori Y, Ito M, Kishi M, Mizutani H, Katada T, Konishi H (2008) Antiallergic constituents from oolong tea stem. Biol Pharm Bull 18(5):683–686. https://doi.org/10.1248/bpb.18.683

  35. Paul S, Wachira FN, Powell W, Waugh R (1997) Diversity and genetic differentiation among populations of Indian and Kenyan tea (Camellia sinensis (L.) O. Kuntze) revealed by AFLP markers. Theor Appl Genet 94(2):255–263. https://doi.org/10.1007/s001220050408

  36. Peakall R, Smouse PE (2012) GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research—an update. Bioinformatics 28(28):2537–2539. https://doi.org/10.1093/bioinformatics/bts460

  37. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959

  38. Rafalski A (2002) Applications of single nucleotide polymorphisms in crop genetics. Curr Opin Plant Biol 5(2):94–100. https://doi.org/10.1016/S1369-5266(02)00240-6

  39. Sun Z, Li H, Zhang Y, Li Z, Ke H, Wu L et al (2018) Identification of SNPs and candidate genes associated with salt tolerance at the seedling stage in cotton (Gossypium hirsutum L.). Front Plant Sci 9:1011. https://doi.org/10.3389/fpls.2018.01011

  40. Takeo T, You X, Wang H, Kinukasa H, Li M, Chen Q (1992) One speculation on thé origin and dispersion of tea plant in China——one speculation based on the chemotaxonomy by using the content-ration of terpen-alcohols found in tea aroma composition. J Tea Sci 12(2):81–86. https://doi.org/10.13305/j.cnki.jts.1992.02.001

  41. Tan LQ, Peng M, Xu LY, Wang LY, Chen SX, Zou Y, Qi GN, Cheng H (2015) Fingerprinting 128 Chinese clonal tea cultivars using SSR markers provides new insights into their pedigree relationships. Tree Genet Genomes 11(5):1–22. https://doi.org/10.1007/s11295-015-0914-6

  42. Taiwan Agricultural Administrative Committee (2019) Farming and Food Administration. https://agrstat.coa.gov.tw/sdweb/public/inquiry/InquireAdvance.aspx. Accessed 1 June 2019

  43. Villordo-Pineda E, González-Chavira MM, Giraldo-Carbajo P, Acosta-Gallegos JA, Caballero-Pérez J (2015) Identification of novel drought-tolerant-associated SNPs in common bean (Phaseolus vulgaris). Front Plant Sci 6:546. https://doi.org/10.3389/fpls.2015.00546

  44. Wambulwa MC, Meegahakumbura MK, Chalo R, Kamunya S, Muchugi A, Xu JC, Liu J, Li DZ, Gao LM (2016) Nuclear microsatellites reveal the genetic architecture and breeding history of tea germplasm of East Africa. Tree Genet Genomes 12(1):1614–2942. https://doi.org/10.1007/s11295-015-0963-x

  45. Wang B, Tan HW, Fang W, Meinhardt LW, Mischke S, Matsumoto T, Zhang D (2015) Developing single nucleotide polymorphism (SNP) markers from transcriptome sequences for identification of longan (Dimocarpus longan) germplasm. Hortic Res 2:14065. https://doi.org/10.1038/hortres.2014.65

  46. Wei C, Yang H, Wang S, Zhao J, Liu C, Gao L, Xia E, Lu Y, Tai Y, She G, Sun J, Cao H, Tong W, Gao Q, Li Y, Deng W, Jiang X, Wang W, Chen Q, Zhang S, Li H, Wu J, Wang P, Li P, Shi C, Zheng F, Jian J, Huang B, Shan D, Shi M, Fang C, Yue Y, Li F, Li D, Wei S, Han B, Jiang C, Yin Y, Xia T, Zhang Z, Bennetzen JL, Zhao S, Wan X (2018) Draft genome sequence of Camellia sinensis var. sinensis provides insights into the evolution of the tea genome and tea quality. Proc Natl Acad Sci U S A 115(18):201719622. https://doi.org/10.1073/pnas.1719622115

  47. Wight W (1959) Nomenclature and classification of the tea plant. Nature 183:1726–1728. https://doi.org/10.1038/1831726a0

  48. Wight W, Barua PK (1957) What is tea? Nature 179(4558):506–507. https://doi.org/10.1038/179506a0

  49. Wu XM, Yao MZ, Ma CL, Wang XC, Chen L (2010) Genetic diversity and population structure among green tea and oolong tea cultivars based on EST-SSR markers. J Tea Sci 30(3):195–202. https://doi.org/10.13305/j.cnki.jts.2010.03.009

  50. Xia EH, Zhang HB, Sheng J, Li K, Zhang QJ, Kim C, Zhang Y et al (2017) The Tea Tree Genome Provides Insights into Tea Flavor and Independent Evolution of Caffeine Biosynthesis. Mol Plant 10(6): 866-877. https://doi.org/10.1016/j.molp.2017.04.002

  51. Xu YQ, Liu PP, Shi J, Gao Y, Wang QS, Yin JF (2018) Quality development and main chemical components of Tieguanyin oolong teas processed from different parts of fresh shoots. Food Chem 249(4):176–183. https://doi.org/10.1016/j.foodchem.2018.01.019

  52. Yan ZQ, Hackman RM, Ensunsa JL, Holt RR, Keen CL (2002) Antioxidative activities of oolong tea. J Agric Food Chem 50(23):6929–6934. https://doi.org/10.1021/jf0206163

  53. Yang Z, Eiji K, Tsuyoshi K, Toshimichi A, Tamaki F, Takamasa I et al (2012) Characterisation of volatile and non-volatile metabolites in etiolated leaves of tea (Camellia sinensis) plants in the dark. Food Chem 135(4):2268–2276. https://doi.org/10.1016/j.foodchem.2012.07.066

  54. Yao MZ, Ma CL, Qiao TT, Jin JQ, Chen L (2012) Diversity distribution and population structure of tea germplasms in China revealed by EST-SSR markers. Tree Genet Genomes 8(1):205–220. https://doi.org/10.1007/s11295-011-0433-z

  55. Zhao DW, Yang JB, Yang SX, Kato K, Luo JP (2014) Genetic diversity and domestication origin of tea plant Camellia taliensis (Theaceae) as revealed by microsatellite markers. BMC Plant Biol 14(1):1471–2229. https://doi.org/10.1186/1471-2229-14-14

  56. Zhou L, Matsumoto T, Tan HW, Meinhardt LW, Mischke S, Wang B et al (2015) Developing single nucleotide polymorphism markers for the identification of pineapple (Ananas comosus) germplasm. Hortic Res 2:15056. https://doi.org/10.1186/1471-2229-14-14

  57. Zhou L, Tan H, Ye NX, Meinhardt LW, Sue M, Li XH et al (2019) Tracing the botanical origin of Fujian white tea using single nucleotide polymorphism (SNP) markers: a model for authenticating premium loose-leaf tea products, Preparing

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Author information

NY, WY, and YL conceived and designed the project. YL, LZ, and XF performed the experiments. YL and WY analyzed the data. YL wrote the manuscript. All authors reviewed and approved the final manuscript.

Correspondence to Wentao Yu or Naixing Ye.

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The authors declare that they have no conflict of interest.

Data archiving statement

All the SNP data of the Oolong tea germplasms used in this work has been made publicly available through the Official Website of Chinese Oolong Tea Industry Innovation Center (http://net.fafu.edu.cn/cotcic/5133/list.htm). The data is also detailed in supplementary file.

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Communicated by A. M. Dandekar

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Lin, Y., Yu, W., Zhou, L. et al. Genetic diversity of oolong tea (Camellia sinensis) germplasms based on the nanofluidic array of single-nucleotide polymorphism (SNP) markers. Tree Genetics & Genomes 16, 3 (2020) doi:10.1007/s11295-019-1392-z

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Keywords

  • Camellia sinensis
  • SNP
  • Oolong tea
  • Population structure
  • Plant germplasms
  • Tea breeding