, 215:162 | Cite as

Combined linkage and association mapping of putative QTLs controlling black tea quality and drought tolerance traits

  • Robert. K. Koech
  • Richard Mose
  • Samson M. Kamunya
  • Zeno ApostolidesEmail author


The advancements in genotyping have opened new approaches for identification and precise mapping of quantitative trait loci (QTLs) in plants, particularly by combining linkage and association mapping (AM) analysis. In this study, a combination of linkage and the AM approach was used to identify and authenticate putative QTLs associated with black tea quality traits and percent relative water content (%RWC). The population structure analysis clustered two parents and their respective 261 F1 progenies from the two reciprocal crosses into two clusters with 141 tea accessions in cluster one and 122 tea accessions in cluster two. The two clusters were of mixed origin with tea accessions in population TRFK St. 504 clustering together with tea accessions in population TRFK St. 524. A total of 71 putative QTLs linked to black tea quality traits and %RWC were detected in interval mapping (IM) method and were used as cofactors in multiple QTL model (MQM) mapping where 46 putative QTLs were detected. The phenotypic variance for each QTL ranged from 2.8 to 23.3% in IM and 4.1 to 23% in MQM mapping. Using Q-model and Q + K-model in AM, a total of 49 DArTseq markers were associated with 16 phenotypic traits. Significant marker-trait association in AM were similar to those obtained in IM, and MQM mapping except for six more putative QTLs detected in AM which are involved in biosynthesis of secondary metabolites, carbon fixation and abiotic stress. The combined linkage and AM approach appears to have great potential to improve the selection of desirable traits in tea breeding.


Quantitative trait loci Tea quality Drought tolerance Linkage mapping Association mapping 



The authors acknowledge the financial support to conduct this research, and study grants for RK and PM from James Finlay (Kenya) Ltd., George Williamson (Kenya) Ltd., Sotik Tea Company (Kenya) Ltd., Mcleod Russell (Uganda) Ltd., the TRI of Kenya and Southern African Biochemistry and Informatics for Natural Products (SABINA). The C. sinensis cultivars used in this study were provided by the TRI of Kenya. Supplementary funding was provided by, the Technology and Human Resources for Industry Programme (THRIP), an initiative of the Department of Trade and Industries of South Africa (dti), the National Research Foundation (NRF) of South Africa, and the University of Pretoria (South Africa).

Author contributions

ZA, SK and RM were involved with the design of the experiment and plant material used. RK was involved in collection of plant material. RK performed the experiments, analyzed samples and interpreted the data. RK wrote the manuscript and revised by RM, SK and ZA. The final manuscript was reviewed and approved by all the authors. The TRI of Kenya and the University of Pretoria had role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Compliance with ethical standards

Conflict of interest

All the authors declare that there is no commercial or financial relationships that can precedence to conflict of interest in research conducted.

Supplementary material

10681_2019_2483_MOESM1_ESM.docx (1.3 mb)
Supplementary material 1 (DOCX 1367 kb)


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Copyright information

© Springer Nature B.V. 2019

Authors and Affiliations

  1. 1.Department of Biochemistry, Genetics and MicrobiologyUniversity of PretoriaPretoriaSouth Africa
  2. 2.Kenya Agriculture and Livestock Research OrganizationTea Research InstituteKerichoKenya
  3. 3.James Finlay (Kenya) LimitedKerichoKenya

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