Characterization of EST-derived SNPs and Development of SNP-markers in Tea (Camellia sinensis)

WANG Li-yuan; ZHANG Cheng-cai; CHENG Hao; WEI Kang

doi:10.13305/j.cnki.jts.2012.04.014

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Journal of Tea Science ›› 2012, Vol. 32 ›› Issue (4) : 369-376. DOI: 10.13305/j.cnki.jts.2012.04.014

Characterization of EST-derived SNPs and Development of SNP-markers in Tea (Camellia sinensis)

WANG Li-yuan, ZHANG Cheng-cai, CHENG Hao^*, WEI Kang

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Abstract

By clustering the 12757 ESTs of tea downloaded from NCBI, a unigene database of tea was successfully built. It was found that the redundancy rate for ESTs from tea was approximately 68.2%. An EST-SNP exploiting system for tea was established preliminarily. The SNP distribution was identified. The occurrence frequency for coding region SNP in tea was appropriately 0.58%. It meant that there was average one SNP in every 200bp of tea ESTs. Furthermore, the hybrid rate for tea genome was deduced to be 0.38%, averagely one hybrid DNA site per 300bp. Totally 818 candidated SNP were exploited from 237 multigene clusters. Then 25 pairs of SNP primers were designed and 75% of these sites were validated to be polymorphism by DNA sequencing.

Key words

Camellia sinensis / EST / SNP / tea plant

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WANG Li-yuan, ZHANG Cheng-cai, CHENG Hao, WEI Kang. Characterization of EST-derived SNPs and Development of SNP-markers in Tea (Camellia sinensis)[J]. Journal of Tea Science. 2012, 32(4): 369-376 https://doi.org/10.13305/j.cnki.jts.2012.04.014

References

[1] 周延清. DNA分子标记技术在植物研究中的应用[M]. 北京: 化学工业出版社, 2005: 2007-2008.
[2] 黄建安, 黄意欢, 罗军武, 等. 茶树多酚氧化酶基因的SNP分析[J]. 湖南农业大学学报, 2007, 33(4): 454-458.
[3] 金基强, 陈亮, 姚明哲, 等. 茶树简化EcoTILLING技术的建立[J]. 茶叶科学, 2010, 30(1): 19-26.
[4] Picoult-Newberg L, Ideker T E, Pohl M G, et al. Mining SNPs from EST databases[J]. Genome Research, 1999, 9: 167-174.
[5] 刘本英, 王平盛, 周红杰, 等. 云南茶组植物ISSR-PCR反应体系的建立[J]. 云南农业大学学报, 2006(增): 21-25.
[6] 史成颖, 宛晓春, 江昌俊, 等. 茶苗嫩根cDNA文库的构建和EST分析[J]. 南京农业大学学报, 2009, 32(1): 126-130.
[7] Sanger F, Nicklen S, Coulson A R.DNA sequencing with chain terminating inhibitors[J]. Proc Natl Acad Sci, 1977, 74(12): 5463-5467.
[8] 张秋生. 基于公共序列数据库的Cucumis属EST-SSR标记的鉴定、开发和利用[D]. 武汉: 华中农业大学, 2006: 30-86.
[9] 张晓红. 桉树EST-SNP的开发及EST图谱的构建[D]. 南京: 南京农业大学, 2009: 31-47.
[10] Varshney R K, Beier U, Khlestkina E K, et al. Single nucleotide polymorphisms in rye (Secal cereal L.): discovery, frequency and applications for genome mapping and diversity studied[J]. Theor. Appl. Genet, 2007, 114(6): 1105-1116.
[11] Somers D J, Kirkpatrick R, Moniwa M, et al. Mining single-nucleotide polymorphisms from hexaploid wheat ESTs[J]. Genome, 2003, 46(3): 431-437.