ORIGINAL PAPER Genomic mapping and testing for quantitative trait loci in tea (Camellia sinensis (L.) O. Kuntze) S. M. Kamunya & F. N. Wachira & R. S. Pathak & R. Korir & V. Sharma & R. Kumar & P. Bhardwaj & R. Chalo & P. S. Ahuja & R. K. Sharma # Springer-Verlag 2010 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 unas- signed markers. No QTL was detected at both sites, which showed strong genotype×site interaction (G×E) but highly effective within-site heritability ( ^ 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 poten- tial 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. Keywords Camellia sinensis . Genotypes × environment interaction . QTL mapping . Tea . Yield . Kenya Introduction Tea is one of the most widely consumed soft beverages in the world and plays a significant role to the economy of all the tea-producing countries, including Kenya where tea is the leading foreign exchange earner and export com- modity. However, the future of tea industry depends upon the availability of high-yielding, black tea quality and drought-tolerant tea clones. The tremendous improvement in Kenyan tea production over the years is largely attributed to development and release of high-yielding and better- quality clones, which have gradually replaced most of the pioneer seedling plantations (Wachira 2002). Kenyan tea has a world-class standing for high black tea quality and Communicated by R. Burdon S. M. Kamunya : V. Sharma : R. Kumar : P. Bhardwaj : P. S. Ahuja : R. K. Sharma (*) Division of Biotechnology, Institute of Himalayan Bioresource Technology, IHBT, (CSIR), Post Box 6, Palampur, Himachal Pradesh 176061, India e-mail: mrk_sharma@yahoo.com e-mail: ramsharma@ihbt.res.in S. M. Kamunya : F. N. Wachira : R. Korir : R. Chalo Tea Research Foundation of Kenya, P.O. Box 820, Kericho 20200, Kenya F. N. Wachira Biochemistry and Molecular Biology Department, Egerton University, P.O. Box 536-20115, Njoro, Kenya R. S. Pathak Department of Crops, Horticulture and Soil Sciences, Egerton University, P.O. Box 536-20115, Njoro, Kenya DOI 10.1007/s11295-010-0301-2 Tree Genetics & Genomes (2010) 6:915–929 Received: 7 November 2008 / Revised: 4 May 2010 / Accepted: 6 May 2010 / Published online: 8 June 2010