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Genome-wide identification of simple sequence repeats and development of polymorphic SSR markers for genetic studies in tea plant (Camellia sinensis)

Abstract

The tea plant (Camellia sinensis (L.) O. Kuntze) is one of the most popular non-alcoholic beverage crops worldwide. The availability of complete genome sequences for the Camellia sinensis var. ‘Shuchazao’ has provided the opportunity to identify all types of simple sequence repeat (SSR) markers by genome-wide scan. In this study, a total of 667,980 SSRs were identified in the ~ 3.08 Gb genome, with an overall density of 216.88 SSRs/Mb. Dinucleotide repeats were predominant among microsatellites (72.25%), followed by trinucleotide repeats (15.35%), while the remaining SSRs accounted for less than 13%. The motif AG/CT (49.96%) and AT/TA (40.14%) were the most and the second most abundant among all identified SSR motifs, respectively; meanwhile, AAT/ATT (41.29%) and AAAT/ATTT (67.47%) were the most common among trinucleotides and tetranucleotides, respectively. A total of 300 primer pairs were designed to screen six tea cultivars for polymorphisms of SSR markers using the five selected repeat types of microsatellite sequences. The resulting 96 SSR markers that yielded polymorphic and unambiguous bands were further deployed on 47 tea cultivars for genetic diversity assessment, demonstrating high polymorphism of these SSR markers. Remarkably, the dendrogram revealed that the phylogenetic relationships among these tea cultivars are highly consistent with their genetic backgrounds or places of origin. The identified genome-wide SSRs and newly developed SSR markers will provide a powerful means for genetic researches in tea plant, including genetic diversity and evolutionary origin analysis, fingerprinting, QTL mapping, and marker-assisted selection for breeding.

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Acknowledgements

This work was supported by the China Postdoctoral Science Foundation (2017M621991), the National Natural Science Foundation of China (31171608), the Natural Science Projects for Colleges and Universities in Anhui Province (KJ2018A0131), the Special Innovative Province Construction in Anhui Province (15czs08032), and the Central Guiding the Science and Technology Development of the Local (2016080503B024). We thank Dr. Enhua Xia for providing sequence alignment between previous SSR markers and the newly developed SSRs.

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Authors

Contributions

SRL performed collections of plant materials, data analysis, and manuscript drafting. YLA was involved in DNA isolation, SSR genotyping, PCR amplifications, and testing amplified fragments. FDL, SJL, and SQZ collected plant materials and conducted identification and analysis of SSRs. LLL and QYZ coordinated collections of plant materials, DNA isolation, and testing amplified fragments. CLW was involved in experimental design and manuscript preparation. All authors read and approved the final manuscript.

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

The 96 sequences containing SSR motif repeats and approximately 300 bp flanking sequence of each SSR motif, each SSR motif was marked in yellow within the sequence (PDF 125 kb)

Online Resource 2

Characteristics of the newly developed 96 SSR markers (PDF 354 kb)

Online Resource 3

Electrophoresis detection to the 47 tea cultivars based on 32 SSR markers. The order of 47 tea cultivars is consistent with the information listed in Table 1, the name of SSR markers and the fragment size of markers were showed on left and right, respectively (PDF 562 kb)

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Liu, S., An, Y., Li, F. et al. Genome-wide identification of simple sequence repeats and development of polymorphic SSR markers for genetic studies in tea plant (Camellia sinensis). Mol Breeding 38, 59 (2018). https://doi.org/10.1007/s11032-018-0824-z

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Keywords

  • Tea (Camellia sinensis)
  • SSR markers
  • Phylogeny
  • Genetic diversity
  • Genome-wide identification