Preliminary Study on SNP Molecular Markers in Tea Chloroplast Genome

LUO Xiangzong; HU Yunfei; WU Linhui; ZHAO Yaqi; ZHENG Weiming; LI Xiangru; LI Li

doi:10.13305/j.cnki.jts.2022.06.012

PDF(1518 KB)

Journal of Tea Science ›› 2022, Vol. 42 ›› Issue (6) : 768-778. DOI: 10.13305/j.cnki.jts.2022.06.012

Research Paper

Preliminary Study on SNP Molecular Markers in Tea Chloroplast Genome

LUO Xiangzong^1,2, HU Yunfei¹, WU Linhui¹, ZHAO Yaqi¹, ZHENG Weiming¹, LI Xiangru³, LI Li^1,*

Author information +

History +

Abstract

The application value of traditional chloroplast gene molecular markers in tea section classification is limited relatively. The aim of this study was to screen out SNP (single nucleotide polymorphism) combinations that could be used for tea plant identification and maternal traceability. In this study, the chloroplast genome sequences of 18 reported tea plants were compared. By designing universal primers, the candidate molecular markers were amplified and analyzed by sanger sequencing in 169 tea cultivars/strains, and 16 pairs of primers containing 25 SNP loci were screened out. This set of SNP molecular markers can be used for maternal traceability and identification analysis of tea cultivars. In addition, the DNA fingerprints composed of SNP sites were digitally encoded in combination with the basic information of tea resources, and finally a 30-digit molecular ID card of tea resources was formed, and corresponding barcodes and two-dimensional codes were constructed for cultivar identification. The data from this study provided a new idea for maternal origin tracing and identification of tea cultivars.

Key words

chloroplast gene / ID card / identification / maternal traceability / SNP molecular markers

Cite this article

EndNote

Ris (Procite)

Bibtex

Download Citations

LUO Xiangzong, HU Yunfei, WU Linhui, ZHAO Yaqi, ZHENG Weiming, LI Xiangru, LI Li. Preliminary Study on SNP Molecular Markers in Tea Chloroplast Genome[J]. Journal of Tea Science. 2022, 42(6): 768-778 https://doi.org/10.13305/j.cnki.jts.2022.06.012

References

[1] Xia E H, Zhang H B, Sheng J, et al.The tea tree genome provides insights into tea flavor and independent evolution of caffeine biosynthesis[J]. Molecular Plant, 2017, 10(6): 866-877.
[2] Raina S N, Ahuja P S, Sharma R K, et al.Genetic structure and diversity of India hybrid tea[J]. Genetic Resources and Crop Evolution. 2012, 59: 1527-1541.
[3] 王让剑, 杨军, 孔祥瑞, 等. 茶树分子标记辅助育种研究进展[J]. 茶叶学报, 2017, 58(4): 157-163.
Wang R J, Yang J, Kong X R, et al.Advances in molecular marker assisted breeding of Camellia sinensis[J]. Acta Tea Sinica, 2017, 58(4): 157-163.
[4] 刘振, 赵洋, 杨阳. 分子标记技术在茶树资源与育种中的研究进展[J]. 茶叶通讯, 2009, 36(3): 30-33.
Liu Z, Zhao Y, Yang Y.Germplasm and breeding research of tea plant based on DNA markers[J]. Journal of Tea Communication, 2009, 36(3): 30-33.
[5] 夏法刚, 衷兴旺, 吴锋, 等. 武夷岩茶种质资源遗传多样性与亲缘关系的SRAP分析[J]. 茶叶科学, 2017, 37(1): 78-85.
Xia F G, Zhong X W, Wu F, et al.SRAP marker analysis of genetic diversity and relationship in Wuyi rock tea germplasm resources[J]. Journal of Tea Science. 2017, 37(1): 78-85.
[6] 陈志丹, 林志坤, 孙威江, 等. 125份武夷山茶树种质资源的遗传多样性分析及DNA指纹图谱的建立[J]. 分子植物育种, 2016, 14(12): 3601-3608.
Chen Z D, Lin Z K, Sun W J, et al.Genetic diversity analysis and DNA fingerprinting construction of 125 tea germplasm resources from Wuyishan[J]. Molecular Plant Breeding, 2016, 14(12): 3601-3608.
[7] Wu G F, Xu X J, Xu J T, et al.Construction of molecular fingerprinting map in gene pool of Jute with SRAP, ISSR, and SSR markers[J]. Acta Agronomica Sinica, 2015, 41(3): 367-377.
[8] Lander E S.The new genomics: global views of biology[J]. Science, 1996, 274(5287): 536-539.
[9] 樊晓静, 于文涛, 蔡春平, 等. 利用SNP标记构建茶树品种资源分子身份证[J]. 中国农业科学, 2021, 54(8): 1751-1760.
Fan X J, Yu W T, Cai C P, et al.Construction of molecular ID for tea cultivars by using of single nucleotide polymorphism (SNP) markers[J]. Scientia Agricultura Sinica, 2021, 54(8): 1751-1760.
[10] 张韵洁, 李德铢. 叶绿体系统发育基因组学的研究进展[J]. 植物分类与资源学报, 2011, 33(4): 365-375.
Zhang Y J, Li D Z.Advances in phylogenomics based on complete chloroplast genomes[J]. Plant Diversity and Resources, 2011, 33(4): 365-375.
[11] McCauley D E, Stevens J E, Peroni P A, et al. The spatial distribution of chloroplast DNA and allozyme polymorphisms within A population of Silene alba (Caryophyllaceae)[J]. American Journal of Botany, 1996, 83(6): 727-731.
[12] Soltis D E, Soltis P S.7-chloroplast DNA and nuclear rDNA variation: insights into autopolyploid and allopolyploid evolution[M]//Kawano S. Biological Approaches and Evolutionary Trends in Plants. Salt Lake City: Academic Press, 1990.
[13] Rousseau-Gueutin M, Bellot S, Martin G, et al.The chloroplast genome of the hexaploid Spartina maritima (Poaceae, Chloridoideae): comparative analyses and molecular dating[J]. Molecular Phylogenetics and Evolution, 2015, 93: 5-16.
[14] Molina J, Hazzouri K M, Nickrent D, et al.Possible loss of the chloroplast genome in the parasitic flowering plant Rafflesia lagascae (Rafflesiaceae)[J]. Molecular Biology and Evolution, 2014, 31(4): 793-803.
[15] Li Y, Zhou J G, Chen X L, et al.Gene losses and partial deletion of small single copy regions of the chloroplast genomes of two hemiparasitic Taxillus species[J]. Scientific Reports, 2017, 7: 12834. doi: 10.1038/s41598-017-13401-4.
[16] Guisinger M M, Kuehl J V, Boore J L, et al.Extreme reconfiguration of plastid genomes in the angiosperm family Geraniaceae: rearrangements, repeats, and codon usage[J]. Molecular Biology and Evolution, 2011, 28(1): 583-600.
[17] Fang W, Yang J B, Yang S X, et al.Phylogeny of Camellia sects. Longipedicellata, Chrysantha and Longissima (Theaceae) based on sequence data of four chloroplast DNA loci[J]. Acta Bot Yunnanica, 2010, 32: 1-13.
[18] Dong W, Liu J, Yu J, et al.Highly variable chloroplast markers for evaluating plant phylogeny at low taxonomic levels and for DNA barcoding[J]. Plos One, 2012, 7(4): e35071. doi: 10.1371/journal.pone.0035071.
[19] Yoon M S, Song Q J, Choi I Y, et al.BARCSoySNP23: a panel of 23 selected SNPs for soybean cultivar identification[J]. Theoretical and Applied Genetics, 2007, 114: 885-899.
[20] 陈亮, 马建强. 茶树非主要农作物品种登记要求及进展[J]. 中国茶叶, 2020, 42(3): 8-12.
Chen L, Ma J Q.Requirement and advance of non-major crop cultivar registration of tea plant[J]. China Tea, 2020, 42(3): 8-12.
[21] Cheng J, Qin C, Tang X, et al.Development of a SNP array and its application to genetic mapping and diversity assessment in pepper (Capsicum spp)[J]. Scientific Reports, 2016, 6: 33293. doi: 10.1038/srep33293.
[22] Wu J, Liu S, Wang Q, et al.Rapid identification of an adult plant stripe rust resistance gene in hexaploid wheat by high-throughput SNP array genotyping of pooled extremes[J]. Theoretical and Applied Genetics, 2018, 31: 43-58.
[23] Schroeder H, Hoeltken A M, Fladung M.Differentiation of Populus species using chloroplast single nucleotide polymorphism (SNP) markers: essential for comprehensible and reliable poplar breeding[J]. Plant Biology, 2012, 14: 374-381.
[24] Schroeder H, Höltken A, Fladung M.Chloroplast SNP-marker as powerful tool for differentiation of Populus species in reliable poplar breeding and barcoding approaches[J]. BMC Proceedings. 2011, 5(s7): 56. doi: 10.1186/1753-6561-5-S7-P56.
[25] 王凤格, 赵久然, 田红丽, 等. 用于玉米母系溯源的一套叶绿体SNP和INDEL分子标记组合: CN106591470A[P].2017-04-26.
Wang F G, Zhao J R, Tian H L, et al. A set of chloroplast SNP and INDEL molecular marker combinations for maternal traceability in maize: CN106591470A[P].2017-04-26.
[26] Jiang L Y, Qian Z Q, Guo Z G, et al.Polyploid origins in Gynostemma pentaphyllum (Cucurbitaceae) inferred from multiple gene sequences[J]. Molecular Phylogenetics & Evolution, 2009, 52(1): 183-191.
[27] 詹梓金. 武夷大红袍种源追溯与基因鉴定[J]. 福建茶叶, 2010, 32(8): 18-20.
Zhan Z J.Provenance tracing and gene identification of Wuyi Dahongpao[J]. Tea in Fujian, 2010, 32(8): 18-20.
[28] Zhang X T, Chen S, Shi L Q, et al.Haplotype-resolved genome assembly provides insights into evolutionary history of the tea plant Camellia sinensis[J]. Nature Genetics, 2021, 53(8): 1250-1259.
[29] 周会, 荆胜利, 李刚, 等. 叶绿体基因组分析在植物系统发育中的应用[J]. 植物学研究, 2014, 3(1): 1-9.
Zhou H, Jin S L, Li G, et al.The applications of chloroplast genome analysis in plant system development[J]. Botanical Research, 2014, 3(1): 1-9.