Oat ( Avena L.) is one of the most important cereal crops in the world, ranked at the sixth top place in planting area and yield among all cereal crops, and possesses high values in food and nutrition, health protection and feeding livestock. Naked oat ( A. nuda) is an endemic type in China. However, a few studies on naked oat germplasm at molecular level have been reported. The aim of this study was to evaluate the genetic diversity of core collection of naked oat using AFLP markers. A total of 281 accessions of naked oat were analyzed using 20 AFLP primer combinations. Selective amplification created 1 137 bands, of which 260 were polymorphic, accounting for 22.96% of the total bands. The mean polymorphism information content (PIC) was 0.0326. For different geographic groups, Simpson's index ranged from 1.235 to 1.495, and Shannon's index varied from 0.1558 to 0.4437. The majority (83.45%) of the AFLP variation resided within accessions of each group, and the rest (16.55%) existed among accessions between groups. The sample size of geographic groups was significantly associated with the number of polymorphic loci, proportion of within-group variation, Simpson's index and Shannon's index. Accessions from Inner Mongolia and Shanxi were most diverse, and those from northeastern China were most distinct. Genetic resemblance was found within accessions from western China. Germplasm from East Europe was genetically close to that from Inner Mongolia, China. The genetic diversity of Chinese accessions was significantly higher than that of exotic accessions. Compared with breeding cultivars, landraces presented a higher proportion of within-group variation. Naked oat landraces were suggested to be collected in the regions where are not well represented by the current collections, and collecting activities should be continuous in the diversity-rich areas such as northwestern and southwestern China in order to enrich naked oat gene pool in China.
