A reduced-representation sequencing method for identifying sex-specific molecular markers in plants with large genomes

Recent advancements in sequencing techniques have significantly enhanced our ability to identify the genomic regions responsible for sex determination in dioecious species. In this context, utilizing reduced-representation genomics analysis (such as ddRAD) as an alternative to whole genome sequencing (WGS) has proven effective in certain plants. In this study, we evaluated the potential of ddRAD along with a dedicated bioinformatics pipeline to identify sex-specific markers in Cycas revoluta, a non-model plant with a large genome. A genomic region associated with sex determination has already been identified through WGS of the related Cycas panzhihuaensis. By comparing the outcomes of our ddRAD pipeline in Cycas revoluta with those from WGS of Cycas panzhihuaensis, we validated the effectiveness of our approach in identifying sex-specific genomic regions in cycads. This research illustrates the efficiency of ddRAD-seq as a rapid method for developing sex-linked molecular markers in non-model plants with large genomes.