Genetic maps are a vital tool in cultivar improvement programmes for woody perennial tree crops such as tea (Camellia sinensis). A population thought to be derived from two known, noninbred parents was scored for RAPD and AFLP markers, in order to develop a linkage map. However, a very high proportion of the markers exhibited unexpected segregation ratios in the light of their configurations in the parents, and an exploratory statistical analysis revealed patterns in the marker scores which can most easily be explained by the hypothesis of three male parents contributing pollen to this cross. We discuss the evidence for this and the subsequent analysis required to assemble the markers from the female parent into the first linkage map for tea. The map has 15 linkage groups of three or more markers, agreeing with the haploid chromosome number of tea. The statistical methods that revealed the subpopulations are easy to apply routinely, and may prove a useful diagnostic tool for the analysis of noninbred mapping populations.
- Cluster analysis