DOI: 10.25338/b8js8d
title: Data from: Rare instances of haploid inducer DNA in potato dihaploids and ploidy-dependent genome instability

description: 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.
description: 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.
description: Supplemental Dataset S1: Description of parents and offspring
 type of progeny of potato dihaploid induction crosses. Each offspring is a
 row in the table. For each offspring, we list the following:
 CIP_ID: Unique identifier number assigned by the
 International Potato Center (CIP). Identifier numbers can be queried
 at http://genebank.cipotato.org/gringlobal/search.aspx to obtain more
 information about each sample. UCD_ID: Internal UC
 Davis identifier number referred to throughout analysis
 at https://github.com/kramundson/MM_manuscript.
 pistil_parent: Breeder code for pistillate parent of each
 progeny. pistil_parent_CIP: CIP identifier number of
 pistillate parent. pollen_parent: Breeder code for
 pollinator parent (haploid inducer) of each progeny.
 pollen_parent_CIP: CIP identifier number of pollinator
 parent. Phureja_marker_phenotype: Presence or absence
 of pollinator-specific "embryo spot" and nodal banding
 phenotype. DH = no spot or banding, PM = spot and/or banding. Prefix
 "ati" if phenotype atypical
 aneuploidy_origin: Aneuploidy status of each progeny. Set to
 "euploid" if no aneuploidy detected in progeny,
 "non-inducer" if aneuploidy of pistillate parent chromosomes
 detected, and "inducer" if aneuploidy of pollinator chromosomes
 detected. ploidy_eval: Ploidy of each offspring
 inferred from flow cytometry or guard cell chloroplast
 counting. snp_ploidy: Ploidy of each offspring
 inferred from whole-genome sequencing
 genomic_hi_perc: Average depth of pollinator allele at SNP loci
 fixed for different alleles in either parent. chrXX:
 Aneuploidy call for a given chromosome. Calls pertain to whole-chromosome
 or segmental gains or losses with parental origin annotated where
 possible. Supplemental Dataset S2:
 Attributes of sequencing libraries generated in this study. For each
 unique combination of biological sample, library preparation, sequencing
 run and sequencing lane, we list the following: 
 UCD_ID: Internal UC Davis identifier number referred to
 throughout analysis
 at https://github.com/kramundson/MM_manuscript.
 parent_breeder_code: If parent, the breeder code of that parent.
 Set to NA for progeny. pistil_parent: Breeder code
 for pistillate parent of each progeny. pollen_parent:
 Breeder code for pollinator parent (haploid inducer) of each
 progeny. B1/I1: Forward index sequence of
 library B2/I2: Reverse index sequence of
 library illumina_id: Illumina instrument, run, chip
 and lane identifier read_type: Type of
 sequencing in_dihaploid_pool: Indicates whether
 library was used in pooling low-coverage dihaploid data. See
 https://github.com/kramundson/MM_manuscript. Library:
 Unique library identifier sequencing_platform: Type
 of instrument sequencing was conducted on.
 spot_count: Raw read count from each sequencing run.
 Supplemental Dataset S3: IGV screenshots of short
 read alignments of putative HI introgression segments in dihaploids MM246,
 MM247 and MM1114, showing an overview of the region, apperance of
 HI-derived haplotypes in the regions, and flanking regions left and right
 of the segment.