Pomegranates, renowned for their fruit, also possess ornamental varieties with unique traits such as double flowering, diverse flower colors, and dwarfing characteristics. Despite their appeal, limited information exists on the genetics and inheritance of these ornamental traits. In this study, we investigated the inheritance and genetic controls of these traits through crosses between the dwarfing cultivar Peppy Le Pom and pomegranate cultivars showcasing ornamental traits. By analyzing multiple families and conducting a genome-wide association study (GWAS) using resequencing data from 64 cultivars, we made several key findings. Firstly, the double flower trait exhibited Mendelian inheritance with a single locus controlling its expression, as evidenced by a 1:1 ratio of double to single flower plants in the F1 generation where a double flower individual was crossed onto a single flower individual. Subsequent analysis identified a SNP within an AP2-like gene on chromosome 3 that was able to differentiate between a single and double flower phenotype. Secondly, flower color inheritance revealed the recessive nature of white flowers compared to orange and red hues. SNPs near a PGLOX gene, previously linked to anthocyanin-less pomegranates, distinguished between white and red/orange flowers, suggesting specific genetic loci involved in determining flower color. Lastly, the dwarfing trait was identified as recessive, exhibiting phenotypic diversity among selfed F1 individuals, indicating potential multiple loci control. Further investigation into the genetic mechanisms governing dwarfing is warranted. In conclusion, our study contributes to understanding the genetic underpinnings of ornamental traits in pomegranates, offering insights valuable for breeding programs aimed at developing novel varieties with desirable ornamental characteristics. Further research into the identified genetic loci promises to enhance our understanding and facilitate targeted breeding efforts in this versatile fruit species.
