Assessment of genome-wide DArT-seq markers for tea Camellia sinensis (L.) O. Kuntze germplasm analysis

Abstract

Tea is the world’s most consumed beverage, next to water. This makes it an economically important crop. However, the genetic relationship between the cultivars at the Tea Research Foundation of Central Africa (TRFCA) have not been classified. This study assessed 56 tea accessions from the TRFCA. The 56 accessions were split into five groups, namely, Cambod type, China type, TRFCA, Tea Research Institute (TRI), and unknown. A total of 16,382 genome-wide genetic markers were developed using a next-generation sequencing (NGS) platform at Diversity Array Technology (DArT). The current study also explored the usefulness of the DArT-seq markers for tea germplasm analysis. The genetic relationships amongst the cultivars were analysed using the neighbour-joining method and UPGMA; this was successful in clustering the different cultivars into groups of origin. Principal coordinate analysis (PCoA) showed that 33 TRFCA-derived cultivars were distributed in all four quadrants. Analysis of molecular variance (AMOVA) revealed that there was a higher proportion of genetic variation (94%) within the groups than there was amongst the groups (6%). Nei’s unbiased genetic distances amongst groups suggested that the 33 TRFCA-derived cultivars had a low genetic distance from the other four groups. This confirms the PCoA inference that the 33 TRFCA had a high genetic admixture. The genetic structure was utilised to assign three cultivars of unknown origin, to the Cambod-type group. Two cultivars were closely related to the China-type group. Our findings are a useful guide for future tea breeding programmes in Southern Africa.