Aneuploidy refers to a condition in which a cell or organism that has an abnormal chromosome number compared to the base chromosome number. This can cause gene dosage imbalances and a potential decrease in fitness. Most potato (Solanum tuberosum) cultivars are tetraploid (2n=4x=48) with a base chromosome number of 12. In this study, we analyzed 1,014 potato genotypes, 422 from two autotetraploid bi-parental full-sib populations and 592 from a diversity panel. We used allele SNP fluorescent intensity data for each individual to determine their ploidy and identify aneuploid individuals using the R package Qploidy. This package estimates the copy number by evaluating the standardized B allele frequencies (BAF) distributions across a sample, chromosome, or chromosome arm. Within the mapping populations, 41% of the members were aneuploids, compared to only 17% of the in the diversity panel; with an average of 27% aneuploidy level across all individuals included in the study. However, the frequency of aneuploidy for any given chromosome was 3%. As a measure of fitness, we compared 19 phenotypic traits related to tuber yield and quality in one of the full-sib mapping populations. There were significant differences between aneuploid and euploid family members for six traits. Aneuploid genotypes had significantly lower total tuber weight/plant, marketable tuber weight/plant, non-marketable tuber number/plant, tuber density, and overall appearance, while having higher percentage of tubers with heat sprouts compared to euploid family members. Chromosome additions were more common than chromosome losses in aneuploid individuals accounting for 57% and 39% of the aneuploid chromosomes, respectively. By analyzing this large potato genotypic dataset (most autotetraploids), we gained a better understanding of patterns of aneuploidy and their impact on crop performance in polyploid crops.
