Impacts of ploidy changes on gene expression in potatoes

Polyploids are organisms with more than two copies of each of their chromosomes. Potato (Solanum tuberosum L.) exhibit ploidy ranging from diploid to pentaploid. For over a century, the United States potato breeders have been developing elite tetraploid clone cultivars to fit specific market class standards. However, genetic gain is slow, and breeding is difficult due to the tetraploid genome's complexity and the difficulty of fixing desirable traits. This has resulted in increasing interest in converting potatoes to a diploid inbred crop. In the US, this process generally starts with the generation of dihaploids (diploids) from tetraploid cultivars. The advantage of this approach is that it facilitates diploid varieties that contain the tetraploid haplotypes previously selected by breeders. However, a change in ploidy is accompanied by a change in the dosage of these haplotypes, which may affect gene expression and resulting phenotypes. To explore the effect of ploidy and dosage change on gene expression we carried out RNA sequencing in dihaploids and their tetraploid parents. We extracted RNA from potato tissues (leaf, tuber, and flower) collected from eighteen tetraploid cultivars and one to two dihaploids generated from each of them. Data were generated using avidity sequencing that resulted in 73-97% mapping of the reads to the potato reference genome. Differentially expressed genes (DEGs) were observed in the tissues based on statistical significance (p≤0.01) and up-regulated with ≥ 1 log₂ fold change (FC), down-regulated with ≤ -1 log₂ FC, and co-expressed with -1≥ log₂ FC ≤ 1 value. In Castle Russet, gene expression in the leaf and tuber tended to be higher in dihaploids (ME05_0047 & ME05_0092) than the tetraploid mother cultivar, whereas the opposite was observed in the flower. Complete results will provide insights into the impact of ploidy change on gene expression in potatoes.