Development of DNA Barcodes for Oaks Using the FRUITFULL Gene

Oaks (genus Quercus, family Fagaceae) are an economically and ecologically important keystone species. Estimation of oak biodiversity and understanding of interactions between oak and other organisms requires accurate species identification. However, identification of oak species can often be challenging due to the morphological similarities between closely related species and the frequency of hybridization throughout the genus. To address this problem, researchers have tested several chloroplast and a handful of nuclear genes; however, these sequences have not yielded enough variation to discriminate between species. Our preliminary analysis of Fagales DNA sequences from Genbank suggests that the Fruitfull gene contains enough sequence variation to identify different oak species. Accordingly, the purpose of this research is to use Fruitfull, a nuclear gene involved in fruit development, to develop DNA barcodes for the identification of oak species. After our initial Alnus-derived primers failed to yield PCR products, a new Quercus lobatae sequence on Genbank served as the source of new primers. Potential primer pairs were selected based on length, GC content, PCR product size, and melting temperatures. Three PCR primer pairs spanning three intron regions were chosen to be tested on a wide range of oak species. Touchdown PCR using these primers and three DNA samples only yielded trace results, so new DNA has been isolated to repeat the experiment. If our results show higher inter-species than intra-species variation and DNA sequence patterns are species-specific, then Fruitfull may prove to be an effective DNA barcode.