Evaluation of polyembryony for genetic resources and efficacy of simple sequence repeat markers for the identification of nucellar and zygotic embryo-derived individuals in citrus

Many citrus cultivars have the polyembryony trait that develops many nucellar embryos alongside a single zygotic embryo in an individual seed by sporophytic apomixis. This unique botanical trait hinders citrus breeding by genetic hybridization and affects breeding efficiency and cost. Techniques to efficiently identify nucellar and zygotic individuals in citrus are still very limited. For a systematic and targeted citrus breeding program, we collected 101 citrus genetic resources and determined their embryo types, which revealed 22 monoembryo, 54 polyembryo, and 25 mixed types. We also developed 17 simple sequence repeat (SSR) markers showing polymorphism among the genetic resources from the public resources and our own comparative genome analysis. Seventeen SSR markers detected a total of 181 alleles, ranging from 5 to 16 alleles per locus. The average polymorphism information content value was 0.67, ranging from 0.43 to 0.84. Genetic cluster analysis based on similarity matrices of alleles revealed that several genetic resources of the genus Citrus were fragmented and/or scattered throughout the entire dendrogram, not forming unique groups, due to frequent natural or intended genetic crossings. Application of these polymorphic SSR markers to F1 individuals derived from several genetic crosses using polyembryonic citrus cultivars as a female parent revealed that the polyembryony trait decreased the breeding efficiency due to the poor occurrence rate of zygotic individuals. Therefore, our results suggest that identification of nucellar and zygotic embryo-derived F1 individuals using SSR markers as a genotyping technology may be a powerful tool for establishing a systematic molecular breeding program in citrus.