Genetic diversity and structure of Ugandan tea (Camellia sinensis (L.) O. Kuntze) germplasm and its implication in breeding

Genetic improvement of tea for both health and economic benefit requires proper genetic characterization of sequence variation present in tea accession especially those conserved in the ex-situ genebanks. Here, we studied the genetic variation and population structure of 376 tea germplasm at Rwebitaba Tea Research Centre (RTRC), a tea research station with the largest collections of tea germplasm in East Africa. The study was conducted using 8480 (22.7%) diversity array technology (DArT) SNP markers. These markers had a high call rate of 77% with mean polymorphic information content (P.I.C) of 0.12 and minor allelic frequency of 0.08. The expected heterozygosity (He) varied from 0.05 to 0.15 while the observed heterozygosity (Ho) varied from 0.01 to 0.26. The overall inbreeding coefficient (FIS) was 0.45, with some populations showing a high level of outcrossing (F-IS = - 0.035). Analysis of molecular variance revealed a high within-population variance (88.9%) showing weak genetic differentiation between populations (PhiPT = 0.111). Structure analysis showed the presence of eight clusters, with all sub-populations highly admixed except for a few tea clones such as Ch-06 and Ch-07. Phylogenetic analysis confirmed the clustering, showing interrelatedness between different tea genotypes, which will facilitate the selection of parents for increased genetic gain and breeding efficiency in tea breeding. In general, the genetic diversity of tea genotypes is relatively low, with high variation within the existing tea populations. These results showed that the existing variation can be exploited for the development of unique tea genotypes in Uganda.