Development of InDel markers based on chloroplast DNA for the identification of Ziziphus jujuba Mill. cultivars

Jujube (Ziziphus jujuba Mill.) is a plant belonging to the genus Ziziphus of the family Rhamnaceae. Z. jujuba is generally rich in nutrients—vitamin C, thiamin, and riboflavin—making it an excellent source of functional food. Z. jujuba cultivation has a long history, resulting in the creation of numerous cultivars, and the economic value of this plant has recently been on the rise. Therefore, there is a need for easy and accurate methods to distinguish the cultivars. We developed insertion or deletion (InDel) markers using chloroplast (CP) DNA to identify Z. jujuba cultivars. A total of 192 InDel loci were found and 21 InDel markers were developed. Twenty-two InDel markers were used for diversity analysis, including the Zj-InDel-1 marker developed in the previous study. The size of the InDel loci varied from 4 to 200 bp. The maximum value of polymorphism information content (PIC) was 0.35, the minimum value was 0.03, and the average was 0.31. The 61 Z. jujuba cultivars were grouped into 8 CP types by the 22 CP InDel markers. The ‘Dongjo’, ‘Sanjo’, ‘Tibetwang’ and ‘Wolgwang’ cultivars were classified independently among the 61 cultivars. The InDel markers developed in this study could be used for cultivar identification and breeding of Z. jujuba.