Development of Species-Specific InDel Markers in Citrus

Citrus taxonomy is complex owing to the existence of a wide range of species: Poncirus is used mainly for rootstock; Fortunella produces small fruit and edible pericarp; and Citrus comprises the most widespread fruit crop species worldwide. Rapidly increasing genome resources from different citrus species facilitate the development of convenient and genome-wide molecular markers that can be applied to both inter- and intra-species analyses. In this study, by comparing the genome sequences of four citrus species, a set of 1958 InDels were identified and 453 candidate InDels were converted into PCR-based markers. Among these candidate InDels, 268 (65%) exhibited length polymorphisms from 30 bp to 200 bp when applied to seven species from the genera Poncirus, Fortunella and Citrus. Seven InDel markers exhibited high intraspecific polymorphisms in a natural pummelo population. The results showed that the InDel markers are effective for both inter- and intra-specific variation and identification analyses. These InDel markers are expected to be applied to germplasm identification, phylogenetic analysis, genetic diversity evaluation and marker-assisted breeding in citrus.