Assessment of Inter Simple Sequence Repeat Markers to Differentiate Sympatric Wild and Domesticated Populations of Common Bean

Abstract

Efficient assessment of genetic diversity is important for conservation and utilization of genetic resources. We sought to assess the ability of inter simple sequence repeats (ISSRs) as molecular markers to identify genetic diversity both within and among sympatric populations of common bean, Phaseolus vulgaris L. One wild and four domesticated populations originating from the Sierra Norte de Puebla, Mexico, were chosen because they were growing in the same region or field. The ISSR diversity was assessed using four primers that revealed a higher number of strong, polymorphic bands in preliminary analyses. Fifty of these bands could be mapped onto the core linkage map in population BAT93 × Jalo EEP558, whereas four were unlinked. The mapped bands were distributed over nine of the 11 linkage groups, suggesting that they were broadly distributed in the genome. On the basis of a sample of 50 intense bands in these five populations, ISSRs were able to clearly distinguish all populations. Most of the variation was distributed among populations rather than within populations, consistent with the predominantly selfing nature of the species. Differentiation among domesticated populations was much higher (FST ≈ 0.49–0.85) than between the wild and domesticated gene pools (FST = 0.05). Within each population, most loci had achieved near‐fixation. Around 7% of individuals showed a lack of correlation between seed type and ISSR fingerprint. Furthermore, each population contained individuals with unusual markers but present in the other populations (frequency < 5 or 10%). Two nonmutually exclusive explanations were discussed—incomplete lineage sorting and introgression—to account for the presence of these unusual individuals. Overall, ISSR markers were very useful to differentiate closely related populations. Further research is necessary to quantify the actual level of outcrossing.