New Insight into Wild Red Raspberry Populations using Simple Sequence Repeat Markers

Abstract

Scottish wild red raspberry (Rubus idaeus) plants at 12 sites were re-examined 10 years after initial studies had been carried out to examine the decline in population size and to address an earlier finding that demonstrated significant population differentiation over a small scale. Ten simple sequence repeat (SSR) loci were screened on the plants and a total of 80 alleles were detected, half of which were unique to a particular population, with all populations containing unique SSR alleles. Only 18 of the 80 alleles present in the wild were found in cultivated raspberries, highlighting the genetic diversity available for future breeding. This finding makes the decline in population number observed a concern, as this unique diversity is being eroded, primarily due to human impact. An additional 17 unique alleles were identified in the cultivars that were not present in the wild individuals studied. Gene flow into one lowland site was identified by the gain of one new allele into progeny at the site, but three alleles were also lost from parents to progeny. SSR markers were used to estimate the levels of outcrossing in wild red raspberry for the first time, and confirmed that the populations studied were outcrossing, intermating populations. The nonsignificant global F IS value indicates that red raspberry is an outbreeder (global F IS = −0.117), but significant population differentiation was observed [global F ST = 0.348 (P < 0.001)]. Diversity in this crop's wild relative and the population differentiation observed may have use in the future for breeding aimed at addressing climate change scenarios, and consideration should be given to means of conserving the diversity revealed by these studies.