Study of SNaPshot Detect SNP Markers in Tea Plant

ZHANG Chengcai; TAN Liqiang; WANG Liyuan; WEI Kang; CHENG Hao

doi:10.13305/j.cnki.jts.2014.02.014

PDF(919 KB)

Journal of Tea Science ›› 2014, Vol. 34 ›› Issue (2) : 180-187. DOI: 10.13305/j.cnki.jts.2014.02.014

Study of SNaPshot Detect SNP Markers in Tea Plant

ZHANG Chengcai¹, TAN Liqiang^1,2, WANG Liyuan¹, WEI Kang¹, CHENG Hao^1,*

Author information +

History +

Abstract

In order to increase the genotyping efficiency of tea SNPs and promote the application of SNPs in tea genetic breeding investigation, the feasibility of SNaPshot in SNPs genotyping of tea plant was investigated. Ten SNPs were selected from previous experiment as target SNPs. Then, these SNPs were detected in different tea cultivars by SNaPshot technology. Six among 10 SNPs were successful detected, with an accuracy of 60%. The polymorphism diversity of these SNPs was also analyzed. The value of N_A was 2, H_e ranged from 0.37 to 0.52, H_o ranged from 0.32 to 0.74, PIC ranged from 0.36 to 0.50. All these markers were shown coincide between `Longjing43` and its repeated test. The markers reported here will be useful for tea genetic linkage map construction and genetic diversity study. The SNaPshot technology will promote the genetic study and accelerate the breeding process in tea plant.

Key words

genetic diversity / genetic linkage map / SNaPshot / SNPs / tea plant

Cite this article

EndNote

Ris (Procite)

Bibtex

Download Citations

ZHANG Chengcai, TAN Liqiang, WANG Liyuan, WEI Kang, CHENG Hao. Study of SNaPshot Detect SNP Markers in Tea Plant[J]. Journal of Tea Science. 2014, 34(2): 180-187 https://doi.org/10.13305/j.cnki.jts.2014.02.014

References

[1] Gupta P K, Roy J K, Prasad M.Single nucleotide polymorphisms (SNPs): a new paradigm in molecular marker technology and DNA polymorphism detection with emphasis on their use in plants[J]. Curr Sci India, 2001, 80(4): 524-535.
[2] Schlötterer C.The evolution of molecular markers—just a matter of fashion?[J] Nat Rev Genet, 2004, 5(1): 63-69.
[3] Hyten D L, Choi I Y, Song Q J, et al. A High Density Integrated Genetic Linkage Map of Soybean and the Development of a 1536 Universal Soy Linkage Panel for Quantitative Trait Locus Mapping[J]. Crop Sci, 2010, 50(3): 960-968.
[4] Delourme R, Falentin C, Fomeju B F, et al. High-density SNP-based genetic map development and linkage disequilibrium assessment in Brassica napus L[J]. BMC Genomics, 2013, 14: 120.
[5] Kuhn D N, Livingstone III D, Main D, et al. Identification and mapping of conserved ortholog set (COS) II sequences of cacao and their conversion to SNP markers for marker-assisted selection in Theobroma cacao and comparative genomics studies[J]. Tree Genet Genomes, 2012, 8(1): 97-111.
[6] Dai F, Nevo E, Wu DZ, et al. Tibet is one of the centers of domestication of cultivated barley[J]. PNAS, 2012, 109(42): 16969-16973.
[7] Sobrino B, Brion M, Carracedo A.SNPs in forensic genetics: a review on SNP typing methodologies[J]. Forensic Sci Int, 2005, 154(2/3): 181-194.
[8] 赵春霞, 石先哲, 张岩, 等. 一种同时检测多个单核苷酸多态性位点的新方法[J]. 分析化学, 2003, 31(8): 906-910.
[9] 胡抗, 袁东亚, 贺学, 等. 分子人类学中的单核苷酸突变检测方法的研究进展[J]. 生命科学, 2013, 25(1): 119-125.
[10] 叶荣菊, 黄志刚, 王讳, 等. SNaPshot技术对萎缩性胃炎IL-1B-1473单核苷酸多态性的检测[J]. 世界华人消化杂志, 2009, 17(12): 1202-1206.
[11] 刘小琦. 采用SNaPshot方法对中国老年黄斑变性与C2和C3基因单核苷酸多态性进行相关性研究[J]. 国际检验医学杂志, 2013, 34(3): 285-290.
[12] 孙亚男, 李安, 史斌. SNaPshot技术检测Y-SNP位点O3-M122单倍群的应用[J]. 中国法医学杂志, 2013, 28(1): 1-4.
[13] Torjek O, Berger D, Meyer RC, et al. Establishment of a high-efficiency SNP-based framework marker set for Arabidopsis[J]. Plant J. 2003, 36(1): 122-140.
[14] Deleu W, Esteras C, Roig C, et al. A set of EST-SNPs for map saturation and cultivar identification in melon[J]. BMC Plant Biol, 2009, 9: 90.
[15] 黄建安, 黄意欢, 罗军武. 茶树多酚氧化酶基因的SNP分析[J]. 湖南农业大学学报: 自然科学版, 2007, 33(4): 455-458.
[16] 王丽鸳, 张成才, 成浩. 茶树EST-SNP分布特征及标记开发[J]. 茶叶科学, 2012, 32(4): 369-376.
[17] 张成才,王丽鸳, 韦康. 基于茶树SNP的dCAPS标记体系研究[J]. 茶叶科学, 2012, 32(6): 517-522.
[18] 张成才. 茶树SNP标记的开发与应用[D]. 北京: 中国农业科学院, 2012.
[19] 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, 21(增) : 21-25.
[20] Botstein D, White R L, Skolnick M.Construction of a genetic linkage map in man using restriction fragment length polymorphisms[J]. Am J Hum Genet, 1980, 32: 314-331.
[21] Chen L, Zhou Z X, Yang Y J.Genetic improvement and breeding of tea plant (Camellia sinensis) in China: from individual selection to hybridization and molecular breeding[J]. Euphytica, 2007, 154: 239-248.
[22] 马建强, 姚明哲, 陈亮. 茶树遗传图谱研究进展[J]. 茶叶科学, 2010, 30(5): 329-335.
[23] Taniguchi F, Furukawa K, Ota-Metoku S.Construction of a high-density reference linkage map of tea (Camellia sinensis)[J]. Breeding Sci, 2012, 62: 263-273.