Development of indel markers from <i>Citrus clementina</i> (Rutaceae) BAC‐end sequences and interspecific transferability in <i>Citrus</i>

• Premise of the study: Indel markers were developed from BAC‐end sequences of Citrus clementina cv. Nules. Transferability and polymorphism were tested in the Citrus genus to estimate the potential of indel markers mined from a single genotype for use in genetic studies. • Methods and Results: Using polyacrylamide gel electrophoresis and DNA silver staining, 89 indel markers were tested for their transferability and polymorphism. Thirty‐eight markers were selected. Heterozygosity in C . clementina cv. Nules was confirmed for 33 of these indel pairs. A preliminary diversity study using a capillary electrophoresis fragment analyzer was conducted with 21 indels using 45 accessions representing Citrus genus diversity. Intraspecific and interspecific polymorphisms were observed. • Conclusions: These results indicate the utility of indel markers developed from sequence data of a single genotype of interspecific origin. In Citrus , these markers will be useful for genetic mapping, germplasm characterization, and phylogenetic assignment of DNA fragments.