ddRADseq applications for Petunia x hybrida clonal line breeding

Molecular genotyping is a key factor for plant breeding programming and Plant Variety Protection. However, its potential still remains to be elucidated when considering orna-mental plants like Petunia x hybrida. In this study, a Petunia breeding clone collection, in-cluding sister line groups, was genotyped through double digest Restriction-site Associ-ated DNA sequencing (ddRADseq), and its genetic diversity and structure were studied. In addition to estimate the high genetic similarity observed among sister lines, this approach allowed the unique discrimination of each clone too. Molecular results were in agreement with genealogy data, assessing the genotyping effectiveness. In addition, the minimal number of variants able to correctly genotype the population was investigated. The variant number could be reduced up to a hundred with minor adjustments in genotyping results. Moreover, analysis of the chromosomal distribution of variants revealed a predominant accumulation in distal regions. Eventually, genetic analyses were repeated considering only variants located in coding sequences and results were in agreement with what pre-viously observed, disclosing the potential of the expressed regions for genotyping purpos-es. Our findings encourage the adoption of high-throughput and cost-effective sequencing techniques for plant genotyping, in order to enhance the technological advancement of breeding programs, in particular for ornamental species.