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Construction of fingerprinting for tea plant (Camellia sinensis) accessions using new genomic SSR markers

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Abstract

As one of the most popular non-alcoholic beverage crops, the tea plant (Camellia sinensis) plays an important role in human health and lifestyle. Genetic fingerprinting based on genomic-derived markers in tea, however, is still in the initial stages, which has limited tea germplasm resource utilization and cultivar protection. In the current study, we identified whole genome-based simple sequence repeat (SSR) loci and successfully developed 36 new genomic SSR markers, which are highly polymorphic with average allele number and polymorphic information content (PIC) of 14.9 and 0.862, respectively. A phylogenetic tree for 80 tea plant accessions was subsequently constructed based on their genotypic scores for these 36 markers. The phylogenetic relationships among the 80 accessions are highly consistent with their genetic backgrounds or original places. Noteworthy, robust fingerprinting power was performed, and the overall probability of finding two random individuals sharing identical genotypes across the 36 loci was estimated to be 1.5 × 10−56. We subsequently identified five SSR markers as a recommended core marker set for fingerprinting the tea plant cultivars or accessions. The combined PI and PIsibs of the marker set were 1.49 × 10−9 and 2.57 × 10−3, respectively, which allowed us to fully discriminate all 80 tea plant accessions from one another. The SSR markers developed here will provide a valuable resource for tea plant genetics and genomic studies, as well as breeding programs. The fingerprinting profiles can serve as a database that is essential for the tea industry and commercial breeding, and for tea plant cultivar identification, utilization, and protection.

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Acknowledgments

This work was supported by the National Natural Science Foundation of China (31171608), the Special Innovative Province Construction in Anhui Province (15czs08032), the Central Guiding the Science and Technology Development of the Local (2016080503B024), and the Anhui Natural Science Foundation (1608085J08, 1608085QC57). We appreciate the anonymous reviewers for constructive comments on this manuscript.

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Author notes

  1. Shengrui Liu and Hongwei Liu contributed equally to this work

Authors and Affiliations

  1. State Key Laboratory of Tea Plant Biology and Utilization/Key Laboratory of Tea Biology and Processing, Ministry of Agriculture, Anhui Agricultural University, West 130 Changjiang Road, Hefei, 230036, Anhui, People’s Republic of China

    Shengrui Liu, Hongwei Liu, Ailin Wu, Yan Hou, Yanlin An & Chaoling Wei

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  1. Shengrui Liu
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  2. Hongwei Liu
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  3. Ailin Wu
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  4. Yan Hou
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  5. Yanlin An
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  6. Chaoling Wei
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Contributions

SRL performed collections of tea plant materials, data analysis, and manuscript drafting. HWL involved in DNA isolation, designing genomic SSRs primers, SSR genotyping, PCR amplifications, and testing amplified fragments. ALW and YH coordinated collections of plant materials and DNA isolation. YLA involved in PCR amplifications and testing amplified fragments. CLW involved in experimental design, data analysis, and manuscript preparation.

Corresponding author

Correspondence to Chaoling Wei.

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The authors declare that they have no competing interests.

Electronic supplementary material

Online Resource 1

Geographic distribution of the 80 tea accessions used in this study. Numbers in parentheses indicate the number of accessions collected from each 13 provinces of China (JPEG 708 kb)

Online Resource 2

Screening of the 36 primer pairs against six selected tea cultivars on 1.5% agarose gels. The cultivars numbered 1 to 6 are ‘Tieguanyin’, ‘Shuchazao’, ‘Longjingchangye’, ‘Yungui’, ‘Yunkang 10’ and ‘Yunmei’, respectively (JPEG 1036 kb)

Online Resource 3

Details of 36 oligonucleotide SSR primer pairs including marker name, type and number of repeat motifs, forward and reverse primer sequences, and expected amplicon sizes (DOCX 17 kb)

Online Resource 4

The fingerprinting profiles of the 80 tea accessions based on five SSR markers (DOCX 21 kb)

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Liu, S., Liu, H., Wu, A. et al. Construction of fingerprinting for tea plant (Camellia sinensis) accessions using new genomic SSR markers. Mol Breeding 37, 93 (2017). https://doi.org/10.1007/s11032-017-0692-y

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