Genetic Diversity and Population Structure of Wild Ribes Populations (Ribes nigrum, Ribes rubrum and Ribes uva-crispa) in the Netherlands Assessed Using MobiSeq Genotyping

The development of effective conservation and management strategies for wild Ribes populations requires a comprehensive understanding of genetic diversity and population structure of these taxa, but only a few genetic studies exist, and these have focused on cultivated material in the genus. We evaluated the use of MobiSeq as a reduced representation sequencing approach to detect genetic variation in three Ribes species, and we used the data to characterize the genetic diversity and population structure in the Netherlands and the relationships between the wild Ribes populations, the ex situ genebank collection, and cultivars. MobiSeq with a single primer designed for repetitive elements that occur in the three species produced 17,000–31,000 SNPs per species after filtering against markers with minor allele frequency (MAF) < 0.01 and markers deviating from Hardy-Weinberg equilibrium (HWE). The SNPs were called against consensus sequences, producing separate sets of markers for each of the species. All three species had moderate genetic diversity (HS = 0.141–0.239) and relatively low differentiation (FST = 0.049–0.083) with no evidence of inbreeding, consistent with their predominantly outcrossing life-history traits. This suggests that Dutch wild populations have largely retained their genetic diversity despite the current habitat fragmentation. Several putatively wild individuals showed evidence of cultivated ancestry, possibly indicating historical introgression or naturalized escapes from cultivation, particularly in R. rubrum and R. uva-crispa. Low differentiation between in situ and ex situ material (FST = 0.004–0.026) suggests that the genebank collections already capture most of the genetic diversity present in wild populations.