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Genomic mapping and testing for quantitative trait loci in tea (Camellia sinensis (L.) O. Kuntze)

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Abstract

The tea industry is significant in the economies of tea-growing countries. Prospects of improving yield of made tea genomic information were explored using clones from a cross between clones TRFCA SFS150 and AHP S15/10. The 42 clones were tested in two distinct tea-growing regions in Kenya. Bulk segregant analysis was performed followed by complete genotyping. Out of 260 informative markers, 100 markers that showed 1:1 segregation were used to construct a linkage map. The map contained 30 (19 maternal and 11 paternal) linkage groups that spanned 1,411.5 cM with mean interval of 14.1 cM between loci. Based on the map, quantitative trait loci (QTL) analysis was done on yield data over 2003–2007 across the two sites, Timbilil and Kangaita. Twenty-three putative QTLs were detected, 16 in five different linkage groups for Timbilil, two in two groups for Kangaita, and the rest were associated with unassigned markers. No QTL was detected at both sites, which showed strong genotype × site interaction (G × E) but highly effective within-site heritability (\( {\hat{h}^2} \) generally > 0.7). Problems of overestimated and spurious QTL effects arising from the smallness of the population should be mitigated by generally high within-site heritability. At least two unassigned markers associated with yield at Kangaita over the whole study period, suggesting potential as candidate markers for site-specific marker-assisted selections. Implications of the results with respect to mapping population, G × E, and marker-assisted selection are discussed.

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References

  • Anon (2002) Tea growers handbook, 5th edn. Tea Research Foundation of Kenya, Kericho

    Google Scholar 

  • Beavis WD (1998) QTL analyses: power, precision and accuracy. In: Paterson AH (ed) Molecular dissection of complex traits. CRC, New York, pp 145–162

    Google Scholar 

  • Bradshaw HD Jr (1998) Case history in genetics of long-lived plants: molecular approaches to domestication of a fast-growing forest tree: Populus. In: Paterson AH (ed) Molecular dissection of complex traits. CRC, New York, pp 219–228

    Google Scholar 

  • Brown GR, Bassoni DL, Gill GP, Fontana JR, Wheeler NC, Megraw RA, Davis MF, Sewell MM, Tuskan GA, Neale DB (2003) Identification of quantitative trait loci influencing wood property traits in loblolly pines (Pinus taeda L.). III. QTL verification and candidate gene mapping. Genetics 164:1537–1546

    CAS  PubMed  Google Scholar 

  • Churchill GA, Doerge RW (1994) Empirical threshold values for quantitative trait mapping. Genetics 138:963–971

    CAS  PubMed  Google Scholar 

  • Collard BCY, Jahufer MZZ, Brouwer JB, Pang ECK (2005) An introduction to markers, quantitative trait loci (QTL) mapping and marker-assisted selection for crop improvement: the concepts. Euphytica 142:169–196

    Article  CAS  Google Scholar 

  • Crouzillat D, Menard B, Mora A, Phillips W, Petiard V (2000) Quantitative trait loci analysis in Theobroma cacao using molecular markers: yield QTL detection and stability over 15 years. Euphytica 114:13–23

    Article  CAS  Google Scholar 

  • Faleiro FG, Queiroz VT, Lopes UV, Guimaraes CT, Pires JL, Yamada MM, Araujo IS, Pereira MG, Schnell R, Filho GAS, Ferreira CF, Barros EG, Moreira MA (2006) Mapping QTLs for witches broom (Crinipellis perniciosa) resistance in cacao (Theobroma cacao L.). Euphytica 149:227–235

    Article  CAS  Google Scholar 

  • Freeman S, West J, James C, Mayes S (2004) Isolation and characterization of highly polymorphic microsatellites in tea (Camellia sinensis). Mol Ecol Notes 4:324–326

    Article  CAS  Google Scholar 

  • Gawel NJ, Jarret RL (1991) A modified CTAB DNA extraction procedure for Musa and Ipomoea. Plant Mol Biol Rep 9:262–266

    Article  CAS  Google Scholar 

  • Gazi MS (1978) Distributional pattern of yield and vacancy of tea in Bangladesh. Tea J 14(2):19–22

    Google Scholar 

  • George MLC, Prasanna BM, Rathore RS, Setty TAS, Kasim F, Azrai M, Vasal S, Balla O, Hautea D, Canama A, Regalado E, Vargas M, Khairallah M, Jeffers D, Hoisington D (2003) Identification of QTLs conferring resistance to downy mildews of maize in Asia. Theor Appl Genet 107:544–551

    Article  CAS  PubMed  Google Scholar 

  • Grattapaglia D, Sederoff RR (1994) Genetic linkage maps of Eucalyptus grandis and Eucalyptus urophylla using pseudo-testcross: mapping strategy and RAPD markers. Genetics 137:1121–1137

    CAS  PubMed  Google Scholar 

  • Hackett C (2002) Statistical methods for QTL mapping in cereals. Plant Mol Biol 80:524–535

    Google Scholar 

  • Hackett CA, Wachira FN, Paul S, Powell W, Waugh R (2000) Construction of a genetic linkage map for Camellia sinensis (tea). Heredity 85:346–355

    Article  CAS  PubMed  Google Scholar 

  • Kamunya SM, Wachira FN (2004) Preliminary observations on inheritance of yield and some physiological traits in tea. Tea 25(2):24–31

    Google Scholar 

  • Kamunya SM, Wachira FN, Chalo RM (2004) Evaluation of newly developed clones of tea (Camellia sinensis) for yields, drought tolerance and quality: Preliminary indications. Tea 25(1):12–19

    Google Scholar 

  • Kearsey MJ, Pooni HS (1996) The genetical analysis of quantitative traits. Stanley Thorne, Cheltenham, p 381

    Google Scholar 

  • Kosambi DD (1944) The estimation of map distances from recombination values. Ann Eugen 12:172–175

    Google Scholar 

  • Lee C (2005) Selection bias in quantitative trait loci mapping. J Hered 96(4):363–367

    Article  CAS  PubMed  Google Scholar 

  • Lerceteau E, Szmidt AE, Anderson B (2001) Detection of quantitative trait loci in Prunus sylvestris L. across years. Euphytica 121:117–122

    Article  Google Scholar 

  • Liu BH (1998) Computational tools for study of complex traits. In: Paterson AH (ed) Molecular detection of complex traits. CRC, Boca Raton, pp 43–79

    Google Scholar 

  • Manly KF, Cudmore RH Jr, Meer JM (2001) Map Manager QTX, Cross-platform software for genetic mapping. Mamm Genome 12:930–932

    Article  CAS  PubMed  Google Scholar 

  • Michelmore RW, Paran I, Kesseli RV (1991) Identification of markers linked to disease-resistance genes by bulked segregant analysis: a rapid method to detect markers in specific genomic regions by using segregating populations. Proc Natl Acad Sci U S A 88:9828–9832

    Article  CAS  PubMed  Google Scholar 

  • Missiaggia AA, Piacezzi AL, Grattapaglia D (2005) Genetic mapping of Eef1, a major effect QTL for early flowering in Eucalyptus grandis. Tree Genet Gen 1:79–84

    Article  Google Scholar 

  • Ortiz R (1996) Statistical basis of marker identification. In: Crouch JH, Tenkouano A (eds) DNA marker-assisted improvement of the staple crops of Sub-Saharan Africa. Proceedings of the Workshop on DNA markers at IITA held by the Crop Improvement Division, IITA, Ibadan, Nigeria, 21–22 August 1996, pp 27–34

  • Sewell MM, Bassoni DL, Megraw RA, Wheeler NC, Neale DB (2000) Identification of QTLs influencing wood property traits in loblolly pine (Pinus taeda L.). I. Physical wood properties. Theor Appl Genet 101:1273–1281

    Article  CAS  Google Scholar 

  • Utz HF, Melchinger AE, Shon CC (2000) Bias and sampling error of the estimated proportion of genotypic variance explained by quantitative trait loci determined from experimental data in maize using cross validation and validation with independent samples. Genetics 154:1839–1849

    PubMed  Google Scholar 

  • Wachira FN (2002) Genetic diversity and characterisation of Kenyan tea germplasm. A tea Genetic Diversity (TGD) project. TGD final project document, Kericho, Kenya

  • Williams CG (1998) QTL mapping in outbred pedigrees. In: Paterson AH (ed) Molecular dissection of complex traits. CRC, New York, pp 81–94

    Google Scholar 

  • Williams JGK, Kubelik AR, Livak KJ, Rafalski JA, Tingey SV (1990) DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res 18:6231–6235

    Article  Google Scholar 

  • Wright JW (1976) Introduction to forest genetics, New York Academic Press, Inc.

  • Yang HY, Korban SS, Kruger J, Schmidt H (1997) The use of modified bulk segregant analysis to identify a molecular marker linked to a scab resistance gene in apple. Euphytica 94:175–182

    Article  Google Scholar 

  • Zabeau M, Vos P (1993) Selective restriction fragment amplification: a general method for DNA fingerprinting. European Patent Application. 92402629 (Publ Number 0 534858 A1)

  • Zeng ZB (1993) Theoretical basis for separation of multiple linked gene effects in mapping quantitative trait loci. Proc Nat Acad Sci U S A 90:10972–10976

    Article  CAS  Google Scholar 

  • Zeng ZB (1994) Precision mapping of quantitative trait loci. Genetics 136:1457–1468

    CAS  PubMed  Google Scholar 

  • Zhang WK, Wang YJ, Luo GZ, Zhang JS, He CY, Wu XL, Gai JY, Chen SY (2004) QTL mapping of ten agronomic traits on the soybean (Glycine max L. Merr.) genetic map and their association with EST markers. Theor Appl Genet 108:1131–1139

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

We would like to thank the Institute of Himalayan Bioresource Technology, IHBT (CSIR), India for providing support and necessary facilities for conducting the molecular work. The first author is thankful to the Council of Scientific and Industrial Research (CSIR), India and the Academy of Sciences for the Developing World (TWAS), Italy, for providing financial assistance in form of Postgraduate CSIR-TWAS Fellowship. The Tea Research Foundation of Kenya also supported the study.

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Authors and Affiliations

  1. Division of Biotechnology, Institute of Himalayan Bioresource Technology, IHBT, (CSIR), Post Box 6, Palampur, Himachal Pradesh, 176061, India

    S. M. Kamunya, V. Sharma, R. Kumar, P. Bhardwaj, P. S. Ahuja & R. K. Sharma

  2. Tea Research Foundation of Kenya, P.O. Box 820, Kericho, 20200, Kenya

    S. M. Kamunya, F. N. Wachira, R. Korir & R. Chalo

  3. Biochemistry and Molecular Biology Department, Egerton University, P.O. Box 536-20115, Njoro, Kenya

    F. N. Wachira

  4. Department of Crops, Horticulture and Soil Sciences, Egerton University, P.O. Box 536-20115, Njoro, Kenya

    R. S. Pathak

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  1. S. M. Kamunya
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  2. F. N. Wachira
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  3. R. S. Pathak
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  4. R. Korir
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  5. V. Sharma
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  6. R. Kumar
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  7. P. Bhardwaj
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  8. R. Chalo
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  9. P. S. Ahuja
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  10. R. K. Sharma
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Corresponding author

Correspondence to R. K. Sharma.

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Communicated by R. Burdon

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Kamunya, S.M., Wachira, F.N., Pathak, R.S. et al. Genomic mapping and testing for quantitative trait loci in tea (Camellia sinensis (L.) O. Kuntze). Tree Genetics & Genomes 6, 915–929 (2010). https://doi.org/10.1007/s11295-010-0301-2

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  • DOI: https://doi.org/10.1007/s11295-010-0301-2

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