Determination of sex-specific DNA sequences in P. atlantica

P. atlantica belongs to the genus Pistacia in the Anacardiaceae family. It has a dioecious flower structure, which means flowers bearing male and female organs are located on separate plants. Besides, it is used as rootstock for pistachio and in industrial and medical fields. This study performed whole-genome resequencing in 15 females and 15 males from the previously obtained P. atlantica species. This study aims to determine sex-specific regions, annotation of sex-related regions, and design a molecular marker that can be used in breeding to distinguish 100% of sex. Quality controls and filtering of the data obtained from sequencing were performed. Coverage values in the 25-30x range were obtained and aligned to the reference genome (P. atlantica). As a result of the alignment, 98% and 99% of the reads were mapped to the genome. As a result of the depth analysis throughout the genome, the sex-specific loci (more than 90% of the reading depth in the total reading in females or males) were analyzed and visualized with the Python and R programming languages. No male-specific loci were found. When the annotations of these determined regions were examined, the genes in the pathways related to flower development were found. For the validation of these loci, SCAR markers were developed from female-specific loci and using these markers, 100 female and 100 male individuals from the germplasm were distinguished with 100% accuracy. In addition, the presence of only female-specific regions and the ZZ/ZW chromosome structure of P. atlantica was revealed in this first study. This study obtained a molecular marker that can be easily applied on agarose gel and works with 100% accuracy, suitable for wide breeding programs in marker-assisted selection studies in P. atlantica species.