Development of Indel markers for the selection of Satsuma mandarin (Citrus unshiu Marc.) hybrids that can be used for low-cost genotyping with agarose gels

Abstract Cross-breeding between cultivars of Satsuma mandarins is difficult because of the seeds’ polyembryonic characteristics. Even if a seed is obtained by hybridization, the seed contains only one zygotic embryo (hybrid embryo) and many nucellar embryos. Therefore, for efficient cross-breeding, it is necessary to select a zygotic embryo from among the nucellar embryos. To identify the zygotic embryo, we have developed 119 Indel markers that can be clearly detected by simple agarose gel electrophoresis by mining the Indel region from the resequencing analysis of the short reads of Satsuma mandarin against the reference genome of Satsuma mandarin . Additionally, we showed that the genotype determined by these markers can be used as an indicator for the selection of zygotic embryo-derived individuals. In addition, many of the developed Indel markers were found to be used for genotyping Satsuma mandarin as well as other citrus species and relatives. This codominant DNA marker that can be detected by low-cost, simple electrophoresis is expected to be used for the identification of zygotic embryo-derived individuals and for various purposes such as cultivar identification.