Rare instances of haploid inducer DNA in potato dihaploids and ploidy-dependent genome instability

In cultivated tetraploid potato, reduction to diploidy (dihaploidy) allows hybridization to diploid germplasm, introgression breeding, and may facilitate the production of inbreds. Pollination with haploid inducers yields maternal dihaploids, as well as triploid and tetraploid hybrids. It is not known if dihaploids result from parthenogenesis, entailing development of embryos from unfertilized eggs, or genome elimination, entailing missegregation and loss of paternal chromosomes. A sign of genome elimination is the occasional persistence of haploid inducer DNA in some of the dihaploids. We characterized the genomes of 919 putative dihaploids and 134 hybrids produced by pollinating tetraploid clones with three haploid inducers, IVP35, IVP101, and PL4. Whole-chromosome or segmental aneuploidy was observed in 76 dihaploids with karyotypes ranging from 2n=2x-1=23 to 2n=2x+3=27. Of 74 aneuploids with additional chromosomes, 66 contained chromosomes from the non-inducer parent and 8 showed chromosomes from the inducer parent. Chromosomal breaks commonly affected the paternal genome in the dihaploid and tetraploid progeny, but not in the triploid progeny. Residual haploid inducer DNA is consistent with genome elimination as the mechanism of haploid induction. Further, the fact that paternal chromosome breaks are specific to dihaploids and tetraploid progeny suggests that they may be specific to 2x sperms, and supports the hypothesis that 2x sperms facilitate genome elimination.

Methods
19 tetraploid potato clones were pollinated with one of three haploid inducer clones (IVP101, IVP35, or PL4) and germinated on soil. Presence or absence of the pollinator-specific "embryo-spot" phenotype was recorded. Genomic DNA was extracted from homogenized leaf tissue and used to construct short-read sequencing libraries. Sequencing data was analyzed using the methods described in Amundson et al., 2020 Genetics (https://doi.org/10.1534/genetics.119.302843) to detect whole chromosome aneuploidy and determine parental origin of aneuploidy when present.